| Previous changeset 14:2b2bfeda00d0 (2020-08-15) Next changeset 16:75342b9ef628 (2021-09-24) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73" |
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modified:
chira_collapse.xml |
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added:
test-data/reads.fastq.gz |
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removed:
test-data/reads.fastq |
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| diff -r 2b2bfeda00d0 -r 00187b27f5e5 chira_collapse.xml --- a/chira_collapse.xml Sat Aug 15 19:07:21 2020 -0400 +++ b/chira_collapse.xml Wed Apr 07 12:41:46 2021 +0000 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@0"> +<tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@1"> <description>deduplicate fastq reads</description> <macros> <import>macros.xml</import> @@ -6,13 +6,18 @@ <expand macro="requirements" /> <command><![CDATA[ chira_collapse.py - -i '$in' + -i + #if $in.ext.endswith(".gz") + <(gunzip -c '$in') + #else + '$in' + #end if -u '$umi_len' -o '$out' ]]></command> <inputs> - <param format="fastq" name="in" type="data" label="Input FASTQ file"/> + <param format="fastq,fastq.gz" name="in" type="data" label="Input FASTQ file"/> <param name="umi_len" type="integer" value="0" label="Length of the UMI if present at the 5' end of your reads"/> </inputs> @@ -22,7 +27,7 @@ <tests> <test expect_num_outputs="1"> - <param name="in" value="reads.fastq" /> + <param name="in" value="reads.fastq.gz" ftype="fastq.gz"/> <output name="out" file="reads.fasta" /> </test> </tests> |
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| diff -r 2b2bfeda00d0 -r 00187b27f5e5 test-data/reads.fastq --- a/test-data/reads.fastq Sat Aug 15 19:07:21 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,96 +0,0 @@ -@183438/1 -TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT -+ -GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG -@397634/1 -TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT -+ -GGGGHHGHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG -@701890/1 -TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT -+ -EEGGHGHHHHHHHHHGGGGGGHGGCGGFGHGHHGGHGGGHGHHHHHHGGGGGGFG -@745414/1 -TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT -+ -GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGF -@753363/1 -TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT -+ -EEEGHHHFHHHHHHHGGFEEFGGGGGGGHHGHHGGHGGFHGHHHHHHGFGGGGGG -@881071/1 -TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT -+ -GGGGHHHHHHHHHHHGGGGGHHGGFGGGHHGHHGGHGGGHGHHHHHHGFGGFHGG -@1059959/1 -TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT -+ -GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG -@1157152/1 -TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT -+ -GGGGHHHHHHHHHHHGGGGGHHGGGGGEHHGHHGGHGGGHGHHHHHHGGGGGHGG -@1295751/1 -TGTTGAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATCAGATACCGTCGTAGT -+ -GGGGHHHHHHHHHHHGGGGGHHGGGGGGHHGHHGGHGGGHGHHHHHHGGGGGHGG -@585749/1 -TGTGGTCATTAATCAAGAACGAAAGTCGGAGGTTCGAAGACGATTAGATACCGTC -+ -GGEGGHHHHHHHHHHHFHHHG?FGEHHGGGFEEHHGHHGGFF?FHGHHHHHGEGG -@1209323/1 -ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA -+ -3AAABFFBBBBBGGEFGGG2AAGHHGGAGHHHHHHHHCHGHHHHHH5GF -@1248864/1 -ATGCAGGGAGGACGATGCGAATGGGGAATCAGGCTAAACAGTTTGAATA -+ -ABBBAF4DAB?BGGEFEFG2AAF3CEGGHHGGFCG33FHFHFHHHHHHH -@475998/1 -CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA -+ -GGEEGB1FFFDGGGFHHHDDFGGHFHEFHHHHFDGGGE?GHFHHHHFHHHDEDHD -@478112/1 -CGCGGTAAAGTGCTTATAGTGCAGGTAGACAGTACTGCCTGCCTTAATGAATGAA -+ -EEFGGFGEHHFGHBBFHHHFGHHHHAGHHHFHFFGEF@BFGGAEHFFHHHGHGHF -@74093/1 -TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA -+ -G?FHHFFHFEFHH3FBAGGC2AAFEEGHFGFDEGGGFEAGFGE5AFF5@@BE5G -@448633/1 -TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA -+ -EFGGFHH5BAFA23AAFFHHDGGHHFGHHHEGHCFGFAFGH3FGGBBG@E@FGF -@849624/1 -TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA -+ -AABFBFFFF2CGDBADEFB2FAFFFHBGHFHDFGHAEGCFFEFDD5GGG@BBFE -@1076923/1 -TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA -+ -GCEFGHHHFEFH23DB553A2BGFFDBBA35FGFFGGGEECGH5DD@@@EBEGF -@1278542/1 -TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA -+ -EGGFHGHHHHGHGEGFHHHHHHFHHHFHGFGHHHHHGGEE3GHGGHGFDBGHHE -@1290525/1 -TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA -+ -CEFFDHH5B2AE2F555532AGF3EGH3AFAEHHFHGD133335DFGH5D@3FF -@1379287/1 -TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA -+ -AEEF1FGHHHGHHFGHHHGG/E1EHHHHGHHFDGGEG?CFGBGEGHHGHHHHHH -@1490590/1 -TGTAGACACAAGGTACACCAATGCCTCTCTGACCACCCATGAGTCTTTGACCTA -+ -GEA3BD5DF2EGCGEDF5EGH3AGHHHFHGFBFHBGGGGH33BFFD555D53FG -@854752/1 -AAAAGACTCTGTAGACATGGCTGGTCTTGAACTCACAGAGATTTGTCTGCCTTTC -+ -G?EFFAF5335DD5B5553222B1A55AFAGHHE33BAF325555A5DF5B3F3B -@1180232/1 -TCAGGACTCTTGGCTGTATCCTTTCCTAAGTGTCTGTCTTCCTTACCACTAACA -+ -EGE0F10B01DDBGC/0BFFGGHHHFE21BA2D221DGHH2DBAGHBDFBG1GF |
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| diff -r 2b2bfeda00d0 -r 00187b27f5e5 test-data/reads.fastq.gz |
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| Binary file test-data/reads.fastq.gz has changed |