Updating workflows/transcriptomics/rnaseq-de from 0.1 to 0.2 #600

gxydevbot · 2024-11-18T05:35:57Z

Hello! This is an automated update of the following workflow: workflows/transcriptomics/rnaseq-de. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.7+galaxy2 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.8+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.1.3.1+galaxy0 should be updated to toolshed.g2.bx.psu.edu/repos/iuc/ggplot2_heatmap2/ggplot2_heatmap2/3.2.0+galaxy1

The workflow release number has been updated from 0.1 to 0.2.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.
Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.
To ignore manual changes and allow autoupdates, delete the branch.

github-actions · 2024-11-18T05:48:04Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	1
Error	0
Failure	0
Skipped	0

Passed Tests

✅ rnaseq-de-filtering-plotting.ga_0

Workflow invocation details

Invocation Messages

Steps

Step 1: Counts from changed condition:
- step_state: scheduled
Step 2: Counts from reference condition:
- step_state: scheduled

Step 11: Differential Analysis:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/deseq2/9a882d108833/deseq2/get_deseq_dataset.R' > /dev/null &&  Rscript '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/deseq2/9a882d108833/deseq2/deseq2.R' --cores ${GALAXY_SLOTS:-1} -o '/tmp/tmpz12vnfdi/job_working_directory/000/10/outputs/dataset_68c0f91c-cfa0-4c43-9a35-3d50f6e082db.dat' -p '/tmp/tmpz12vnfdi/job_working_directory/000/10/outputs/dataset_85aa60fa-bcad-46eb-87d5-a47d4cb672a3.dat' -A 0.1 -n '/tmp/tmpz12vnfdi/job_working_directory/000/10/outputs/dataset_2f8a5393-62c6-4052-816b-6ee3379a9676.dat'              -H  -f '[["DEFactor", [{"BaseFactor": ["/tmp/tmpz12vnfdi/files/4/3/e/dataset_43eb9297-810e-41c7-a8ca-6146e3d4e819.dat", "/tmp/tmpz12vnfdi/files/c/8/4/dataset_c849c55e-b6f5-4071-ad64-07865a53b5b4.dat"]}, {"MainFactor": ["/tmp/tmpz12vnfdi/files/e/a/2/dataset_ea2c1d5d-b714-4932-8ce7-e9711931600d.dat", "/tmp/tmpz12vnfdi/files/b/6/0/dataset_b601ca20-9f26-46fe-930c-a35dc9610462.dat"]}]]]' -l '{"dataset_ea2c1d5d-b714-4932-8ce7-e9711931600d.dat": "SRR5085169 Counts Table", "dataset_b601ca20-9f26-46fe-930c-a35dc9610462.dat": "SRR5085170 Counts Table", "dataset_43eb9297-810e-41c7-a8ca-6146e3d4e819.dat": "SRR5085167 Counts Table", "dataset_c849c55e-b6f5-4071-ad64-07865a53b5b4.dat": "SRR5085168 Counts Table"}' -t 1

Exit Code:

```
0
```

Standard Error:

estimating size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Warning message:
`aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.

Standard Output:

primary factor: DEFactor 

---------------------
No size factor was used
DESeq2 run information

sample table:
                          DEFactor
SRR5085167 Counts Table BaseFactor
SRR5085168 Counts Table BaseFactor
SRR5085169 Counts Table MainFactor
SRR5085170 Counts Table MainFactor

design formula:
~DEFactor


4 samples with counts over 7127 genes
Applied default - beta prior off
[1] "use_beta_prior is set to FALSE"
using disperion fit type: parametric 
creating plots
summary of results
DEFactor: MainFactor vs BaseFactor

out of 5734 with nonzero total read count
adjusted p-value < 0.1
LFC > 0 (up)       : 2, 0.035%
LFC < 0 (down)     : 13, 0.23%
outliers [1]       : 0, 0%
low counts [2]     : 2963, 52%
(mean count < 7)
[1] see 'cooksCutoff' argument of ?results
[2] see 'independentFiltering' argument of ?results

NULL
closing plot device
null device 
          1 
Session information:

R version 4.3.1 (2023-06-16)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.23.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

time zone: NA
tzcode source: system (glibc)

attached base packages:
[1] stats4    tools     stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] pheatmap_1.0.12             ggrepel_0.9.3              
 [3] ggplot2_3.4.2               rjson_0.2.21               
 [5] gplots_3.1.3                RColorBrewer_1.1-3         
 [7] DESeq2_1.40.2               SummarizedExperiment_1.30.2
 [9] Biobase_2.60.0              MatrixGenerics_1.12.2      
[11] matrixStats_1.0.0           GenomicRanges_1.52.0       
[13] GenomeInfoDb_1.36.1         IRanges_2.34.1             
[15] S4Vectors_0.38.1            BiocGenerics_0.46.0        
[17] getopt_1.20.3              

loaded via a namespace (and not attached):
 [1] utf8_1.2.3              generics_0.1.3          bitops_1.0-7           
 [4] KernSmooth_2.23-22      gtools_3.9.4            lattice_0.21-8         
 [7] caTools_1.18.2          magrittr_2.0.3          grid_4.3.1             
[10] Matrix_1.6-0            fansi_1.0.4             scales_1.2.1           
[13] codetools_0.2-19        cli_3.6.1               rlang_1.1.1            
[16] crayon_1.5.2            XVector_0.40.0          munsell_0.5.0          
[19] withr_2.5.0             DelayedArray_0.26.6     S4Arrays_1.0.4         
[22] parallel_4.3.1          BiocParallel_1.34.2     dplyr_1.1.2            
[25] colorspace_2.1-0        locfit_1.5-9.8          GenomeInfoDbData_1.2.10
[28] vctrs_0.6.3             R6_2.5.1                lifecycle_1.0.3        
[31] zlibbioc_1.46.0         pkgconfig_2.0.3         pillar_1.9.0           
[34] gtable_0.3.3            glue_1.6.2              Rcpp_1.0.11            
[37] tibble_3.2.1            tidyselect_1.2.0        farver_2.1.1           
[40] labeling_0.4.2          compiler_4.3.1          RCurl_1.98-1.12

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
advanced_options	`{"auto_mean_filter_off": false, "esf_cond": {"__current_case__": 0, "esf": ""}, "fit_type": "1", "outlier_filter_off": false, "outlier_replace_off": false, "prefilter_conditional": {"__current_case__": 1, "prefilter": ""}, "use_beta_priors": false}`
batch_factors	`None`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
header	`true`
output_options	`{"alpha_ma": "0.1", "output_selector": ["pdf", "normCounts"]}`
select_data	`{"__current_case__": 1, "how": "datasets_per_level", "rep_factorName": [{"__index__": 0, "factorName": "DEFactor", "rep_factorLevel": [{"__index__": 0, "countsFile": {"values": [{"id": 1, "src": "hdca"}]}, "factorLevel": "MainFactor"}, {"__index__": 1, "countsFile": {"values": [{"id": 2, "src": "hdca"}]}, "factorLevel": "BaseFactor"}]}]}`
tximport	`{"__current_case__": 1, "tximport_selector": "count"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c7<", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 2, "component_value": "0.1", "select_param_type": "float"}}]`
dbkey	`"?"`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "abs(c3)>", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 2, "component_value": "0.5", "select_param_type": "float"}}]`
dbkey	`"?"`

Step 14: toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.1.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/e98d4ab5b5bc/deg_annotate/deg_annotate.py' -in '/tmp/tmpz12vnfdi/files/6/8/c/dataset_68c0f91c-cfa0-4c43-9a35-3d50f6e082db.dat' -m 'degseq' -g '/tmp/tmpz12vnfdi/files/8/7/2/dataset_8727b6a8-cbb4-46a6-bd79-0dc199104131.dat' -t 'exon' -i 'gene_id' -x 'transcript_id' -a 'gene_biotype, gene_name' -o '/tmp/tmpz12vnfdi/job_working_directory/000/13/outputs/dataset_a40cfd0a-a90c-443f-bc5f-48d90f3cfec1.dat'

Exit Code:

```
0
```

Standard Output:

DE(X)Seq output file     : /tmp/tmpz12vnfdi/files/6/8/c/dataset_68c0f91c-cfa0-4c43-9a35-3d50f6e082db.dat
Input file type          : degseq
Annotation file          : /tmp/tmpz12vnfdi/files/8/7/2/dataset_8727b6a8-cbb4-46a6-bd79-0dc199104131.dat
Feature type             : exon
ID attribute             : gene_id
Transcript attribute     : transcript_id
Attributes to include    : gene_biotype, gene_name
Annotated output file    : /tmp/tmpz12vnfdi/job_working_directory/000/13/outputs/dataset_a40cfd0a-a90c-443f-bc5f-48d90f3cfec1.dat

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
advanced_parameters	`{"gff_attributes": "gene_biotype, gene_name", "gff_feature_attribute": "gene_id", "gff_feature_type": "exon", "gff_transcript_attribute": "transcript_id"}`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode	`"degseq"`

Step 15: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpz12vnfdi/job_working_directory/000/14/configs/tmpjoibxu0z' '/tmp/tmpz12vnfdi/files/2/f/8/dataset_2f8a5393-62c6-4052-816b-6ee3379a9676.dat' > '/tmp/tmpz12vnfdi/job_working_directory/000/14/outputs/dataset_74e4165f-1682-4435-939b-15206ca2fa46.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"END{print NF}"`
dbkey	`"?"`

Step 16: Annotate DESeq2 table:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpz12vnfdi/files/9/4/3/dataset_943262f7-06a4-46a3-b2a9-ca2c09cd6642.dat' >> '/tmp/tmpz12vnfdi/job_working_directory/000/15/outputs/dataset_ea5df634-5102-43c7-895f-804d0e82d223.dat' && cat '/tmp/tmpz12vnfdi/files/a/4/0/dataset_a40cfd0a-a90c-443f-bc5f-48d90f3cfec1.dat' >> '/tmp/tmpz12vnfdi/job_working_directory/000/15/outputs/dataset_ea5df634-5102-43c7-895f-804d0e82d223.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 15, "src": "hda"}]}}]`

Step 17: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"text"`
remove_newlines	`true`

Step 18: Filter with p-adj threshold:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpz12vnfdi/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpz12vnfdi/files/e/a/5/dataset_ea5df634-5102-43c7-895f-804d0e82d223.dat' '/tmp/tmpz12vnfdi/job_working_directory/000/18/outputs/dataset_97245f12-45f9-477c-a596-c33ce24cbf92.dat' '/tmp/tmpz12vnfdi/job_working_directory/000/18/configs/tmpusvgoh25' 13 "str,float,float,float,float,float,float,str,int,int,str,str,str" 1

Exit Code:

```
0
```

Standard Output:

Filtering with c7<0.1, 
kept 0.22% of 7128 valid lines (7128 total lines).
Skipped 4356 invalid line(s) starting at line #2773: "YDL246C	0.164326158122698	0.855789798651137	4.98087080202474	0.171815297498433	0.863582738705987	NA	chrIV	8682	9756	-	protein_coding	SOR2"

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"c7<0.1"`
dbkey	`"?"`
header_lines	`"1"`

Step 19: Generate Valcanot plot of DE genes:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

Rscript '/tmp/tmpz12vnfdi/job_working_directory/000/17/configs/tmp8hjj249e'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
Removed 1393 rows containing missing values (geom_point).

Standard Output:

null device 
          1 
R version 4.0.5 (2021-03-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS/LAPACK: /usr/local/lib/libopenblasp-r0.3.15.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggrepel_0.9.1 ggplot2_3.3.3 dplyr_1.0.6  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6       magrittr_2.0.1   tidyselect_1.1.1 munsell_0.5.0   
 [5] colorspace_2.0-1 R6_2.5.0         rlang_0.4.11     fansi_0.5.0     
 [9] grid_4.0.5       gtable_0.3.0     utf8_1.2.1       withr_2.4.2     
[13] ellipsis_0.3.2   digest_0.6.27    tibble_3.1.2     lifecycle_1.0.0 
[17] crayon_1.4.1     purrr_0.3.4      farver_2.1.0     vctrs_0.3.8     
[21] glue_1.4.2       labeling_0.4.2   compiler_4.0.5   pillar_1.6.1    
[25] generics_0.1.0   scales_1.1.1     pkgconfig_2.0.3

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fdr_col	`"7"`
header	`"yes"`
label_col	`"13"`
labels	`{"__current_case__": 0, "label_select": "signif", "top_num": "10"}`
lfc_col	`"3"`
lfc_thresh	`"0.5"`
out_options	`{"rscript_out": false}`
plot_options	`{"boxes": false, "legend": null, "legend_labs": "Down,Not Sig,Up", "title": null, "xlab": null, "xmax": null, "xmin": null, "ylab": null, "ymax": null}`
pval_col	`"6"`
signif_thresh	`"0.1"`

Step 20: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c1-c", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 0, "component_value": "5", "select_param_type": "text"}}]`
dbkey	`"?"`

Step 3: Count files have header:
- step_state: scheduled

Step 21: Filter with log2 FC threshold:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpz12vnfdi/galaxy-dev/tools/stats/filtering.py' '/tmp/tmpz12vnfdi/files/9/7/2/dataset_97245f12-45f9-477c-a596-c33ce24cbf92.dat' '/tmp/tmpz12vnfdi/job_working_directory/000/19/outputs/dataset_f5010fea-0590-4a64-a483-2f1b0b2e3488.dat' '/tmp/tmpz12vnfdi/job_working_directory/000/19/configs/tmproewlyq2' 13 "str,float,float,float,float,float,float,str,int,int,str,str,str" 1

Exit Code:

```
0
```

Standard Output:

Filtering with abs(c3)>0.5, 
kept 93.75% of 16 valid lines (16 total lines).

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cond	`"abs(c3)>0.5"`
dbkey	`"?"`
header_lines	`"1"`

Step 22: join1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpz12vnfdi/galaxy-dev/tools/filters/join.py' '/tmp/tmpz12vnfdi/files/2/f/8/dataset_2f8a5393-62c6-4052-816b-6ee3379a9676.dat' '/tmp/tmpz12vnfdi/files/f/5/0/dataset_f5010fea-0590-4a64-a483-2f1b0b2e3488.dat' 1 1 '/tmp/tmpz12vnfdi/job_working_directory/000/20/outputs/dataset_d32c0796-1d68-4833-8b87-e033a10dc9c2.dat'   --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpz12vnfdi/job_working_directory/000/20/configs/tmpuxq5n2ex -H

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
field1	`"1"`
field2	`"1"`
fill_empty_columns	`{"__current_case__": 0, "fill_empty_columns_switch": "no_fill"}`
header	`"-H"`
partial	`""`
unmatched	`""`

Step 23: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpz12vnfdi/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpz12vnfdi/files/d/3/2/dataset_d32c0796-1d68-4833-8b87-e033a10dc9c2.dat' 'c1-c5' T '/tmp/tmpz12vnfdi/job_working_directory/000/22/outputs/dataset_2b2355c0-e0e8-4403-a1ef-19e5049bcca5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c1-c5"`
dbkey	`"?"`
delimiter	`"T"`

Step 24: Generate Heatmap of counts:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpz12vnfdi/job_working_directory/000/23/configs/tmpoy833em5' && Rscript '/tmp/tmpz12vnfdi/job_working_directory/000/23/configs/tmpoy833em5'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Standard Output:

options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

library("RColorBrewer")
library("gplots")

input <- read.delim('/tmp/tmpz12vnfdi/files/2/b/2/dataset_2b2355c0-e0e8-4403-a1ef-19e5049bcca5.dat', sep='\t', header=TRUE)

mat_input <- data.matrix(input[,2:ncol(input)])
rownames(mat_input) <- input[,1]

    linput <- log2(mat_input+1)

    scale <- "none"

srtCol <- 30
    rlabs <- FALSE
    clabs <- NULL
    label_margins <- c(8,1)

    dendrogramtoplot <- "both"
        reorder_cols <- TRUE
        reorder_rows <- TRUE
        # Layout is:
        # 4 = color key           | 3 = dendrogram for columns
        # 2 = dendrogram for rows | 1 = heatmap
        layout_matrix <- rbind(c(4,3), c(2,1))
        key_margins <- list(mar=c(4,0.5,2,1))
        lheight <- c(1, 5)
        lwidth <- c(1,3)
    hclust_fun <- function(x) hclust(x, method='complete')
        dist_fun <- function(x) dist(x, method='euclidean')

ncolors <- 50
    colused <- colorRampPalette(c("#ffffff", "#ff0000"))(ncolors)

    pdf(file='/tmp/tmpz12vnfdi/job_working_directory/000/23/outputs/dataset_321621a0-1792-4d69-b7a7-a408d2b92b0a.dat')

heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
    distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
    col=colused, trace="none", density.info = "none", margins=label_margins,
    main = '', cexCol=0.8, cexRow=0.8, srtCol=srtCol,
    keysize=3, key.xlab='', key.title='', key.par=key_margins,
    lmat=layout_matrix, lhei=lheight, lwid=lwidth)

dev.off()
        null device 
          1

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_cond	`{"__current_case__": 0, "cluster": "yes", "cluster_cols_rows": "both", "clustering": "complete", "distance": "euclidean"}`
colorchoice	`{"__current_case__": 1, "color1": "#ffffff", "color2": "#ff0000", "type": "two"}`
dbkey	`"?"`
image_file_format	`"pdf"`
key	`""`
labels	`"columns"`
title	`""`
transform	`"log2plus1"`
zscore_cond	`{"__current_case__": 0, "scale": "none", "zscore": "none"}`

Step 25: Generate Heatmap of Z-scores:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpz12vnfdi/job_working_directory/000/24/configs/tmpk3xixofh' && Rscript '/tmp/tmpz12vnfdi/job_working_directory/000/24/configs/tmpk3xixofh'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored

Attaching package: ‘gplots’

The following object is masked from ‘package:stats’:

    lowess

Standard Output:

options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")

library("RColorBrewer")
library("gplots")

input <- read.delim('/tmp/tmpz12vnfdi/files/2/b/2/dataset_2b2355c0-e0e8-4403-a1ef-19e5049bcca5.dat', sep='\t', header=TRUE)

mat_input <- data.matrix(input[,2:ncol(input)])
rownames(mat_input) <- input[,1]

    linput <- mat_input

    linput <- t(apply(linput, 1, scale))
    colnames(linput) <- colnames(input)[2:ncol(input)]
    rownames(linput) <- input[,1]
    scale <- "none"

srtCol <- 30
    rlabs <- FALSE
    clabs <- NULL
    label_margins <- c(8,1)

    dendrogramtoplot <- "both"
        reorder_cols <- TRUE
        reorder_rows <- TRUE
        # Layout is:
        # 4 = color key           | 3 = dendrogram for columns
        # 2 = dendrogram for rows | 1 = heatmap
        layout_matrix <- rbind(c(4,3), c(2,1))
        key_margins <- list(mar=c(4,0.5,2,1))
        lheight <- c(1, 5)
        lwidth <- c(1,3)
    hclust_fun <- function(x) hclust(x, method='complete')
        dist_fun <- function(x) dist(x, method='euclidean')

ncolors <- 50
    colused <- colorRampPalette(c("#0000ff", "#ffffff", "#ff0000"))(ncolors)

    pdf(file='/tmp/tmpz12vnfdi/job_working_directory/000/24/outputs/dataset_cdb2d506-529c-4aeb-9759-926ffb34a107.dat')

heatmap.2(linput, dendrogram=dendrogramtoplot, Colv=reorder_cols, Rowv=reorder_rows,
    distfun=dist_fun, hclustfun=hclust_fun, scale = scale, labRow = rlabs, labCol = clabs,
    col=colused, trace="none", density.info = "none", margins=label_margins,
    main = '', cexCol=0.8, cexRow=0.8, srtCol=srtCol,
    keysize=3, key.xlab='', key.title='', key.par=key_margins,
    lmat=layout_matrix, lhei=lheight, lwid=lwidth)

dev.off()
        null device 
          1

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
cluster_cond	`{"__current_case__": 0, "cluster": "yes", "cluster_cols_rows": "both", "clustering": "complete", "distance": "euclidean"}`
colorchoice	`{"__current_case__": 2, "color1": "#0000ff", "color2": "#ffffff", "color3": "#ff0000", "type": "three"}`
dbkey	`"?"`
image_file_format	`"pdf"`
key	`""`
labels	`"columns"`
title	`""`
transform	`"none"`
zscore_cond	`{"__current_case__": 1, "zscore": "rows"}`

Step 4: Gene Annotaton:
- step_state: scheduled
Step 5: Adjusted p-value threshold:
- step_state: scheduled

Step 6: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

times=1; yes -- 'GeneID__tc__Base mean__tc__log2(FC)__tc__StdErr__tc__Wald-Stats__tc__P-value__tc__P-adj__tc__Chromosome__tc__Start__tc__End__tc__Strand__tc__Feature__tc__Gene name' 2>/dev/null | head -n $times >> '/tmp/tmpz12vnfdi/job_working_directory/000/6/outputs/dataset_61d0427f-6a80-463f-bbe7-455c45adad70.dat';

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
token_set	`[{"__index__": 0, "line": "GeneID\tBase mean\tlog2(FC)\tStdErr\tWald-Stats\tP-value\tP-adj\tChromosome\tStart\tEnd\tStrand\tFeature\tGene name", "repeat_select": {"__current_case__": 0, "repeat_select_opts": "user", "times": "1"}}]`

Step 7: log2 fold change threshold:
- step_state: scheduled

Step 8: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 2, "default_value": "0.05", "param_type": "float", "pick_from": [{"__index__": 0, "value": "0.1"}]}}`

Step 9: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

sed --sandbox -r -f '/tmp/tmpz12vnfdi/job_working_directory/000/8/configs/tmp0wyalgm8' '/tmp/tmpz12vnfdi/files/6/1/d/dataset_61d0427f-6a80-463f-bbe7-455c45adad70.dat' > '/tmp/tmpz12vnfdi/job_working_directory/000/8/outputs/dataset_943262f7-06a4-46a3-b2a9-ca2c09cd6642.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
adv_opts	`{"__current_case__": 0, "adv_opts_selector": "basic"}`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"s/__tc__/\\t/g"`
dbkey	`"?"`

Step 10: toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"2770ba06a57011ef9545c98e6440421e"`
chromInfo	`"/tmp/tmpz12vnfdi/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
style_cond	`{"__current_case__": 1, "pick_style": "first_or_default", "type_cond": {"__current_case__": 2, "default_value": "1.0", "param_type": "float", "pick_from": [{"__index__": 0, "value": "0.5"}]}}`

Other invocation details
- history_id
  - 6c1a105ff0beebf7
- history_state
  - ok
- invocation_id
  - 6c1a105ff0beebf7
- invocation_state
  - scheduled
- workflow_id
  - 6c1a105ff0beebf7

Updating workflows/transcriptomics/rnaseq-de from 0.1 to 0.2

389e47a

fix changelog header

05790cc

lldelisle approved these changes Nov 18, 2024

View reviewed changes

lldelisle merged commit 45843b7 into galaxyproject:main Nov 18, 2024
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Updating workflows/transcriptomics/rnaseq-de from 0.1 to 0.2 #600

Updating workflows/transcriptomics/rnaseq-de from 0.1 to 0.2 #600

gxydevbot commented Nov 18, 2024

github-actions bot commented Nov 18, 2024

Workflow invocation details

Updating workflows/transcriptomics/rnaseq-de from 0.1 to 0.2 #600

Updating workflows/transcriptomics/rnaseq-de from 0.1 to 0.2 #600

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gxydevbot commented Nov 18, 2024

github-actions bot commented Nov 18, 2024

Test Results (powered by Planemo)

Test Summary

Workflow invocation details