Mercurial > repos > iuc > bcftools_query_list_samples

annotate bcftools_query_list_samples.xml @ 13:77e0bd62b554 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
author iuc
date Thu, 14 Oct 2021 10:26:00 +0000
parents 473f814b74d5
children 57c0f25c6fcb
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1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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1 <?xml version='1.0' encoding='utf-8'?>
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473f814b74d5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 2684e1443f03bfe2ae20c31d23817415ec8f7e69
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2 <tool name="bcftools List Samples" id="bcftools_@EXECUTABLE@_list_samples" version="@TOOL_VERSION@">
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1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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3 <description>in VCF/BCF file</description>
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77e0bd62b554 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit d5a01866d60f9775392420988259f1e79c464163"
iuc
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4 <expand macro="bio_tools" />
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1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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5 <macros>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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6 <token name="@EXECUTABLE@">query</token>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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7 <import>macros.xml</import>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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8 </macros>
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9 <expand macro="requirements" />
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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10 <expand macro="version_command" />
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11 <command detect_errors="aggressive"><![CDATA[
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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12 @PREPARE_ENV@
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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13 @PREPARE_INPUT_FILE@
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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14 bcftools @EXECUTABLE@ --list-samples
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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15 ## Primary Input/Outputs
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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16 @INPUT_FILE@
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17 | tee $output_file | tr '\n' ','
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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18 ]]>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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19 </command>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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20 <inputs>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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21 <expand macro="macro_input" />
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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22 </inputs>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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23 <outputs>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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24 <data name="output_file" format="tabular"/>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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25 </outputs>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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26 <tests>
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27 <test>
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28 <param name="input_file" ftype="vcf" value="query.vcf" />
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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29 <output name="output_file">
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30 <assert_contents>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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31 <has_text text="C" />
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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32 <not_has_text text="A" />
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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33 </assert_contents>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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34 </output>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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35 </test>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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36 </tests>
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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37 <help><![CDATA[
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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38 =====================================
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39 bcftools List Samples @EXECUTABLE@
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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40 =====================================
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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41
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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42 Lists Samples from a VCF/BCF file
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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43
1af52ffc90e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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44 @BCFTOOLS_MANPAGE@#@EXECUTABLE@
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45
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46 @BCFTOOLS_WIKI@
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47 ]]>
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48 </help>
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49 <expand macro="citations" />
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50 </tool>