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Updating pairtools from 1.0.3 to 1.1.0 (galaxyproject#5974)
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* Updating tools/pairtools from version 1.0.3 to 1.1.0

* Updated test data and minor changes as per new release

* Version bump

* Updated test data for sort and split

* Updated Suffix Version

Co-authored-by: Björn Grüning <[email protected]>

* Minor change

Co-authored-by: Björn Grüning <[email protected]>

---------

Co-authored-by: planemo-autoupdate <[email protected]>
Co-authored-by: Björn Grüning <[email protected]>
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@SaimMomin12 @bgruening
3 people authored Apr 30, 2024
1 parent 252f4cc commit 162c595
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Showing 23 changed files with 1,849 additions and 870 deletions.
2 changes: 1 addition & 1 deletion tools/pairtools/dedup.xml
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]]></command>
<inputs>
<param name="pairs_path" type="data" format="4dn_pairs,4dn_pairsam" label="Input pairs file" help="Input triu-flipped sorted .pairs or .pairsam file"/>
<param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="False" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>
<param argument="--mark-dups" type="boolean" truevalue="--mark-dups" falsevalue="" checked="True" label="Duplicate pairs are marked as DD in pair_type and as a duplicate in the SAM entries"/>
<param argument="--output-dups" type="boolean" truevalue="--output-dups" falsevalue="" checked="False" label="Output file for duplicate pairs"/>
<param argument="--output-stats" type="boolean" truevalue="--output-stats" falsevalue="" checked="False" label="Output file for duplicate statistics"/>
</inputs>
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2 changes: 1 addition & 1 deletion tools/pairtools/macros.xml
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<macros>
<token name="@TOOL_VERSION@">1.0.3</token>
<token name="@TOOL_VERSION@">1.1.0</token>
<token name="@SUFFIX_VERSION@">0</token>
<xml name="edam_ontology">
<edam_datas>
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2 changes: 1 addition & 1 deletion tools/pairtools/parse.xml
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<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy1" profile="23.2" license="MIT">
<tool id="pairtools_parse" name="Pairtools parse" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="23.2" license="MIT">
<description>Find ligation pairs in alignments and create pairs.</description>
<macros>
<import>macros.xml</import>
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8 changes: 4 additions & 4 deletions tools/pairtools/test-data/output_dedup_pairs.pairsam
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#samheader: @PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.00.1.fastq.gz MATalpha_R1.lane1.00.2.fastq.gz
#samheader: @PG ID:pairtools_parse-1.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa VN:1.0.2
#samheader: @PG ID:pairtools_sort-1.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-1.2 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-1.3 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-1.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-1.3 VN:1.1.0
#samheader: @PG ID:bwa-2CCE5976 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane1.01.1.fastq.gz MATalpha_R1.lane1.01.2.fastq.gz
#samheader: @PG ID:pairtools_parse-2.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-2CCE5976 VN:1.0.2
#samheader: @PG ID:pairtools_sort-2.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-2.2 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-2.3 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-2.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-2.3 VN:1.1.0
#samheader: @PG ID:bwa-3CAFD9D9 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.00.1.fastq.gz MATalpha_R1.lane2.00.2.fastq.gz
#samheader: @PG ID:pairtools_parse-3.2 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:bwa-3CAFD9D9 VN:1.0.2
#samheader: @PG ID:pairtools_sort-3.3 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-3.2 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-3.3 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-3.4 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-3.3 VN:1.1.0
#samheader: @PG ID:bwa-4548A671 PN:bwa VN:0.7.15-r1140 CL:bwa mem -t 8 -v 3 -SP sacCer3.fa.gz MATalpha_R1.lane2.01.1.fastq.gz MATalpha_R1.lane2.01.2.fastq.gz
#samheader: @PG ID:samtools PN:samtools PP:bwa-4548A671 VN:1.19.2 CL:samtools view -s 0.1 -b -@ 4 -o subset.bam test.bam
#samheader: @PG ID:pairtools_parse-4.3 PN:pairtools_parse CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools parse -o output_parsed_pairs_bam.pairs --output-stats output_parsed_pairs.stats --min-mapq 40 --walks-policy 5unique --max-inter-align-gap 30 --chroms-path test.reduced.chrom.sizes test.bam PP:samtools VN:1.0.2
#samheader: @PG ID:pairtools_sort-4.4 PN:pairtools_sort CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools sort -o output_sorted_pairs.pairsam output_parsed_pairs_bam.pairs PP:pairtools_parse-4.3 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/scratch/ddepanis/Software/anaconda3/envs/MAP_env/bin/pairtools dedup -o output_dedup_pairs.pairsam output_sorted_pairs.pairsam PP:pairtools_sort-4.4 VN:1.0.2
#samheader: @PG ID:pairtools_dedup-4.5 PN:pairtools_dedup CL:/usr/local/bin/pairtools dedup /tmp/tmpp1v7bap4/files/2/1/3/dataset_21372a8a-66a4-4ab8-8a38-a1e4d87d5048.dat -o /tmp/tmpp1v7bap4/job_working_directory/000/2/outputs/dataset_b7034ba7-f57e-4752-a341-425fdb4da81e.dat --nproc-in 1 --nproc-out 1 PP:pairtools_sort-4.4 VN:1.1.0
#columns: readID chrom1 pos1 chrom2 pos2 strand1 strand2 pair_type sam1 sam2
HWI-ST560:29:B0A7LABXX:2:1101:15566:24141 chrI 3199 chrI 3399 + - UU HWI-ST560:29:B0A7LABXX:2:1101:15566:2414197chrI31996015S35M=3350201CTTAGACAATAAGCTAGCTTTCAAGATATAAGATACGAAATAGGGGTTGA111442422223232232<FHIIIIBCCFHEHFHHIHCGIJIDHHJ?@FHNM:i:0MD:Z:35AS:i:35XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:15566:24141145chrI33506050M=3199-201TAGAATCTCCCATGTCAACGGGTTTCCATACCTCCCCAGCATCATACATCGHHGFAGFJJJIHHFGD?HIGCGHGHHHFAFC<IHFACHDAFDEDADB==NM:i:0MD:Z:50AS:i:50XS:i:0Yt:Z:UU
HWI-ST560:29:B0A7LABXX:2:1101:18861:21891 chrI 35431 chrI 35703 + - UU HWI-ST560:29:B0A7LABXX:2:1101:18861:2189197chrI354316050M=35654273GACCACGTGGTCGTTGATGCTGCCAGCAGTTGTGCAGACCTGCATTGCTG114442222322<2@FEAFHFH<CFHFFH?GH:CDHGGIGEFDG<BBH9?NM:i:1MD:Z:35G14AS:i:45XS:i:0Yt:Z:UU HWI-ST560:29:B0A7LABXX:2:1101:18861:21891145chrI356546050M=35431-273ATGTGGCTGCTTTAATTGAGCCTCTTTCTGTCACCTGGCATGCTGTTAAG>EGDD?BFIIIIGBHCJIJIHFIHFHGHGGC<2GHGHFD<HFFDDDDB@BNM:i:1MD:Z:14G35AS:i:45XS:i:0Yt:Z:UU
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