Mercurial > repos > iuc > bcftools_query_list_samples

annotate bcftools_query_list_samples.xml @ 21:a14ff44b60c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 96c0663be587b73bdf09ddf060cb559f28f9eba7
author iuc
date Thu, 12 Jan 2023 15:23:13 +0000
parents cd1e861304f5
children ac880195825d
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46efc6a53967 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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2 <tool name="bcftools List Samples" id="bcftools_@EXECUTABLE@_list_samples" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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3 <description>in VCF/BCF file</description>
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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4 <macros>
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5 <token name="@EXECUTABLE@">query</token>
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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6 <import>macros.xml</import>
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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7 </macros>
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9dbaefd7e08f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit af43d9cf6824f88726900857116f333ff4cdd336"
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8 <expand macro="bio_tools" />
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46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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9 <expand macro="requirements" />
46efc6a53967 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" />
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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11 <command detect_errors="aggressive"><![CDATA[
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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12 @PREPARE_ENV@
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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13 @PREPARE_INPUT_FILE@
46efc6a53967 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
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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15 ## Primary Input/Outputs
46efc6a53967 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' ','
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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18 ]]>
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19 </command>
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20 <inputs>
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21 <expand macro="macro_input" />
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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22 </inputs>
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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23 <outputs>
46efc6a53967 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"/>
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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25 </outputs>
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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" />
46efc6a53967 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>
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31 <has_text text="C" />
46efc6a53967 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" />
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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33 </assert_contents>
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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34 </output>
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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35 </test>
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36 </tests>
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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37 <help><![CDATA[
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38 =====================================
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39 bcftools List Samples @EXECUTABLE@
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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40 =====================================
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41
46efc6a53967 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
46efc6a53967 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
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43
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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>