Mercurial > repos > iuc > chira_collapse

annotate chira_collapse.xml @ 16:46b2b4780d5c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 07:49:43 +0000
parents 8ab9137aa5c1
children 3c9284df3fa3
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8ab9137aa5c1 "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">
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f5dd3ee488f6 "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>
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46b2b4780d5c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <command><![CDATA[
f5dd3ee488f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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9 chira_collapse.py
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10 -i
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11 #if $in.ext.endswith(".gz")
8ab9137aa5c1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
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12 <(gunzip -c '$in')
8ab9137aa5c1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
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13 #else
8ab9137aa5c1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
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14 '$in'
8ab9137aa5c1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 030e4e8e72dc37ccd64702e093e949d18899ad73"
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15 #end if
0
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16 -u '$umi_len'
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17 -o '$out'
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18 ]]></command>
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20 <inputs>
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21 <param format="fastq,fastq.gz" name="in" type="data" label="Input FASTQ file"/>
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22 <param name="umi_len" type="integer" value="0"
f5dd3ee488f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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23 label="Length of the UMI if present at the 5' end of your reads"/>
f5dd3ee488f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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24 </inputs>
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25 <outputs>
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26 <data format="fasta" name="out" label="ChiRA collapse FASTQ on ${on_string}"/>
f5dd3ee488f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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27 </outputs>
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29 <tests>
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30 <test expect_num_outputs="1">
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31 <param name="in" value="reads.fastq.gz" ftype="fastq.gz"/>
0
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32 <output name="out" file="reads.fasta" />
f5dd3ee488f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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33 </test>
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34 </tests>
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36 <help>
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38 .. class:: infomark
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39
f5dd3ee488f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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40 **What it does**
f5dd3ee488f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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f5dd3ee488f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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42 This tool deduplicates the reads from the FASTQ file and writes into a fasta each read once with it's read count.
f5dd3ee488f6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit e4f841daf49048d6c656d50cffb344b53eebeec2"
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44 **Inputs**
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45
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46 * Quality and adapter trimmed FASTQ file
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48 **Outputs**
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49
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50 * 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
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52 </help>
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53 <expand macro="citations" />
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54 </tool>