Mercurial > repos > iuc > chira_collapse

annotate 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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
15
00187b27f5e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
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1 <tool id="chira_collapse" name="ChiRA collapse" version="@WRAPPER_VERSION@1">
0
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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2 <description>deduplicate fastq reads</description>
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <command><![CDATA[
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8 chira_collapse.py
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9 -i
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10 #if $in.ext.endswith(".gz")
00187b27f5e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
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11 <(gunzip -c '$in')
00187b27f5e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
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12 #else
00187b27f5e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
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13 '$in'
00187b27f5e5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
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14 #end if
0
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15 -u '$umi_len'
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16 -o '$out'
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17 ]]></command>
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18
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19 <inputs>
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20 <param format="fastq,fastq.gz" name="in" type="data" label="Input FASTQ file"/>
0
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21 <param name="umi_len" type="integer" value="0"
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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22 label="Length of the UMI if present at the 5' end of your reads"/>
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23 </inputs>
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24 <outputs>
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25 <data format="fasta" name="out" label="ChiRA collapse FASTQ on ${on_string}"/>
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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26 </outputs>
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27
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28 <tests>
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29 <test expect_num_outputs="1">
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30 <param name="in" value="reads.fastq.gz" ftype="fastq.gz"/>
0
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31 <output name="out" file="reads.fasta" />
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32 </test>
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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33 </tests>
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35 <help>
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37 .. class:: infomark
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38
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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39 **What it does**
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40
872249f5495a "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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41 This tool deduplicates the reads from the FASTQ file and writes into a fasta each read once with it's read count.
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42
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43 **Inputs**
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44
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45 * Quality and adapter trimmed FASTQ file
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47 **Outputs**
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48
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49 * FASTA file with unique sequences. The headers of the sequence are in the following format: >sequence_id|UMI|read_count
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51 </help>
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52 <expand macro="citations" />
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53 </tool>