Mercurial > repos > iuc > get_hrun

annotate get_hrun.xml @ 0:ccb3b00e6405 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
author iuc
date Tue, 02 Mar 2021 21:35:15 +0000
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ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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1 <?xml version="1.0"?>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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2 <tool id="get_hrun" name="Get homopolymer run length" version="@VERSION@+galaxy0" profile="@PROFILE@" license="MIT">
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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3 <description>Annotate indel variants with homopolymer context</description>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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4 <macros>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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5 <import>macros.xml</import>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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6 </macros>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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7 <expand macro="requirements"/>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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8 <command detect_errors="exit_code"><![CDATA[
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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9 ln -s '${reference}' ref.fa &&
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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10 samtools faidx ref.fa &&
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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11 python '${__tool_directory__}/get_hrun.py' --reference ref.fa --in-vcf '${in_vcf}' --out-vcf '${out_vcf}'
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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12 ]]></command>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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13 <inputs>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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14 <param argument="--in-vcf" type="data" format="vcf" label="Input VCF"/>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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15 <param argument="--reference" type="data" format="fasta" label="Input Reference FASTA"/>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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16 </inputs>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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17 <outputs>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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18 <data name="out_vcf" format="vcf" label="${tool.name} on ${on_string}"/>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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19 </outputs>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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20 <tests>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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21 <test>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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22 <param name="in_vcf" value="in.vcf"/>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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23 <param name="reference" value="reference.fasta"/>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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24 <output name="out_vcf" value="out.vcf"/>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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25 </test>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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26 </tests>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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27 <help><![CDATA[
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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28 .. class:: infomark
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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29
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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30 **What it does**
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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31
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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32 @WID@
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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33
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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34 **Inputs**
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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35 - VCF file
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
iuc
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36 - Reference file for that VCF
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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37 **Outputs**
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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38 - VCF with annotated homopolymers
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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39 ]]></help>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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40 <expand macro="citations"/>
ccb3b00e6405 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun commit 5810d89666698dbe49ef17c334799fce76823621"
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41 </tool>