Skip to content

Commit

Permalink
Updating the Stringtie tool and test dataset (#5981)
Browse files Browse the repository at this point in the history 
* Updating tools/stringtie from version 2.2.1 to 2.2.2

* Updated tool version and test dataset

* Minor changes

* Updated test params

---------

Co-authored-by: planemo-autoupdate <[email protected]>
  • Loading branch information
@SaimMomin12
SaimMomin12 and planemo-autoupdate authored Apr 30, 2024
1 parent b8bc892 commit 252f4cc
Show file tree
Hide file tree
Showing 16 changed files with 335 additions and 335 deletions.
6 changes: 3 additions & 3 deletions tools/stringtie/macros.xml
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
<macros>
<token name="@TOOL_VERSION@">2.2.1</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@TOOL_VERSION@">2.2.2</token>
<token name="@VERSION_SUFFIX@">0</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@TOOL_VERSION@">stringtie</requirement>
<requirement type="package" version="1.16.1">samtools</requirement>
<requirement type="package" version="1.20">samtools</requirement>
<yield/>
</requirements>
</xml>
Expand Down
180 changes: 90 additions & 90 deletions tools/stringtie/stringtie.xml
View file

Large diffs are not rendered by default.

40 changes: 20 additions & 20 deletions tools/stringtie/stringtie_merge.xml
View file
Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
<tool id="stringtie_merge" name="StringTie merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
<description>transcripts</description>
<xrefs>
<xref type="bio.tools">stringtie</xref>
</xrefs>
<macros>
<import>macros.xml</import>
</macros>
<xrefs>
<xref type="bio.tools">stringtie</xref>
</xrefs>
<expand macro="requirements" />
<expand macro="stdio" />
<expand macro="version_command" />
Expand All @@ -26,35 +26,35 @@
-o '$out_gtf' '$inputs'
]]></command>
<inputs>
<param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format" />
<param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging" />
<param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge" />
<param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge" />
<param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge" />
<param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge" />
<param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction" />
<param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together" />
<param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them" />
<param name="input_gtf" type="data" format="gtf,gff3" multiple="true" label="Transcripts" help="In GTF or GFF3 format"/>
<param name="guide_gff" argument="-G" type="data" format="gtf,gff3" optional="true" label="Reference annotation to include in the merging"/>
<param name="min_len" argument="-m" type="integer" min="0" value="50" label="Minimum input transcript length to include in the merge"/>
<param name="min_cov" argument="-c" type="integer" min="0" value="0" label="Minimum input transcript coverage to include in the merge"/>
<param name="min_fpkm" argument="-F" type="float" min="0" value="1" label="Minimum input transcript FPKM to include in the merge"/>
<param name="min_tpm" argument="-T" type="float" min="0" value="1" label="Minimum input transcript TPM to include in the merge"/>
<param name="min_iso" argument="-f" type="float" value="0.01" label="Minimum isoform fraction"/>
<param name="gap_len" argument="-g" type="integer" value="250" label="Gap between transcripts to merge together"/>
<param name="keep_introns" argument="-i" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Keep merged transcripts with retained introns" help="By default these are not kept unless there is strong evidence for them"/>
</inputs>
<outputs>
<data name="out_gtf" format="gtf" />
<data name="out_gtf" format="gtf"/>
</outputs>
<tests>
<test>
<param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf" />
<param name="guide_gff" ftype="gtf" value="stringtie_in.gtf" />
<output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" compare="re_match" sort="true"/>
<param name="input_gtf" ftype="gtf" value="stringtie_out1.gtf,stringtie_out2.gtf,stringtie_out3.gtf,stringtie_out4.gtf"/>
<param name="guide_gff" ftype="gtf" value="stringtie_in.gtf"/>
<output name="out_gtf" file="stringtie_merge_out1.gtf" ftype="gtf" lines_diff="2"/>
</test>
<test>
<param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
<param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/>
<param name="guide_gff" ftype="gtf" value="stringtie_merge_in3.gtf" />
<output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" compare="re_match" sort="true"/>
<output name="out_gtf" file="stringtie_merge_out2.gtf" ftype="gtf" lines_diff="4"/>
</test>
<test>
<param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf" />
<param name="input_gtf" ftype="gtf" value="stringtie_merge_in1.gtf,stringtie_merge_in2.gtf"/>
<output name="out_gtf" ftype="gtf">
<assert_contents>
<has_text text="stringtie --merge" />
<has_text text="stringtie --merge"/>
</assert_contents>
</output>
</test>
Expand Down
12 changes: 6 additions & 6 deletions tools/stringtie/test-data/stringtie_merge_out1.gtf
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# StringTie version 2\.2\.1
# stringtie --merge -p [0-9]+ -G /[-_/a-zA-Z0-9]+\.dat -m 50 -c 0 -F 1\.0 -T 1\.0 -f 0\.01 -g 250 -o /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat /[-_/a-zA-Z0-9]+\.dat
test_chromosome\tStringTie\texon\t351\t400\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+";
test_chromosome\tStringTie\texon\t501\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+";
test_chromosome\tStringTie\texon\t53\t250\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; exon_number "[0-9]+"; ref_gene_id "CUFF\.[0-9]+";
test_chromosome\tStringTie\ttranscript\t53\t550\t1000\t\+\t\.\tgene_id "MSTRG\.[0-9]+"; transcript_id "CUFF\.[0-9]+\.1"; ref_gene_id "CUFF\.[0-9]+";
# stringtie --merge -p 1 -G /tmp/tmpr8yl388j/files/d/8/3/dataset_d8325888-f757-4336-9e42-1101c6ec296d.dat -m 50 -c 0 -F 1.0 -T 1.0 -f 0.01 -g 250 -o /tmp/tmpr8yl388j/job_working_directory/000/6/outputs/dataset_51c0f399-1d26-44c7-a4fd-e6f8897fe843.dat /tmp/tmpr8yl388j/files/5/5/b/dataset_55be25a6-c7f0-474e-a011-bb4cd427cfa2.dat /tmp/tmpr8yl388j/files/b/2/e/dataset_b2ef2a9d-3640-4858-8424-b4a29c57164d.dat /tmp/tmpr8yl388j/files/d/9/b/dataset_d9be016a-da47-4ad1-89bd-e9781f2751db.dat /tmp/tmpr8yl388j/files/b/e/f/dataset_befee6d4-95fb-4ee9-83a4-9b1302e6a21a.dat
# StringTie version 2.2.2
test_chromosome StringTie transcript 53 550 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; ref_gene_id "CUFF.1";
test_chromosome StringTie exon 53 250 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "1"; ref_gene_id "CUFF.1";
test_chromosome StringTie exon 351 400 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "2"; ref_gene_id "CUFF.1";
test_chromosome StringTie exon 501 550 1000 + . gene_id "MSTRG.1"; transcript_id "CUFF.1.1"; exon_number "3"; ref_gene_id "CUFF.1";
Loading

0 comments on commit 252f4cc

Please sign in to comment.