Mercurial > repos > iuc > chira_collapse

changeset 15:00187b27f5e5 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
author iuc
date Wed, 07 Apr 2021 12:41:46 +0000
parents 2b2bfeda00d0
children 75342b9ef628
files chira_collapse.xml test-data/reads.fastq test-data/reads.fastq.gz
diffstat 3 files changed, 9 insertions(+), 100 deletions(-) [+]
line wrap: on
line diff
--- 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>
--- a/test-data/reads.fastq	Sat Aug 15 19:07:21 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
Binary file test-data/reads.fastq.gz has changed