Mercurial > repos > iuc > chira_collapse

comparison chira_collapse.xml @ 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 872249f5495a
children 75342b9ef628
comparison
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14:2b2bfeda00d0 15:00187b27f5e5
1 <tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@0"> 1 <tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@1">
2 <description>deduplicate fastq reads</description> 2 <description>deduplicate fastq reads</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command><![CDATA[ 7 <command><![CDATA[
8 chira_collapse.py 8 chira_collapse.py
9 -i '$in' 9 -i
10 #if $in.ext.endswith(".gz")
11 <(gunzip -c '$in')
12 #else
13 '$in'
14 #end if
10 -u '$umi_len' 15 -u '$umi_len'
11 -o '$out' 16 -o '$out'
12 ]]></command> 17 ]]></command>
13 18
14 <inputs> 19 <inputs>
15 <param format="fastq" name="in" type="data" label="Input FASTQ file"/> 20 <param format="fastq,fastq.gz" name="in" type="data" label="Input FASTQ file"/>
16 <param name="umi_len" type="integer" value="0" 21 <param name="umi_len" type="integer" value="0"
17 label="Length of the UMI if present at the 5' end of your reads"/> 22 label="Length of the UMI if present at the 5' end of your reads"/>
18 </inputs> 23 </inputs>
19 <outputs> 24 <outputs>
20 <data format="fasta" name="out" label="ChiRA collapse FASTQ on ${on_string}"/> 25 <data format="fasta" name="out" label="ChiRA collapse FASTQ on ${on_string}"/>
21 </outputs> 26 </outputs>
22 27
23 <tests> 28 <tests>
24 <test expect_num_outputs="1"> 29 <test expect_num_outputs="1">
25 <param name="in" value="reads.fastq" /> 30 <param name="in" value="reads.fastq.gz" ftype="fastq.gz"/>
26 <output name="out" file="reads.fasta" /> 31 <output name="out" file="reads.fasta" />
27 </test> 32 </test>
28 </tests> 33 </tests>
29 34
30 <help> 35 <help>