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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538"
author iuc
date Sun, 19 Dec 2021 15:47:57 +0000
parents 75342b9ef628
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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05996586c8b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 8064fa653fe73c9432c76783d6c635d86548d538"
iuc
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1 <tool id="chira_collapse" name="ChiRA collapse" version="@TOOL_VERSION@1">
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2 <description>deduplicate fastq reads</description>
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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="bio_tools"/>
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7 <expand macro="requirements" />
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8 <command><![CDATA[
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9 chira_collapse.py
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10 -i
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11 #if $in.ext.endswith(".gz")
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12 <(gunzip -c '$in')
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13 #else
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14 '$in'
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15 #end if
0
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16 -u '$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"/>
0
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22 <param name="umi_len" type="integer" value="0"
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23 label="Length of the UMI if present at the 5' end of your reads"/>
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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}"/>
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27 </outputs>
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28
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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"/>
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32 <output name="out" file="reads.fasta" />
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33 </test>
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34 </tests>
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36 <help>
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37
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38 .. class:: infomark
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39
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40 **What it does**
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41
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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.
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43
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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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47
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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>