annotate vcf2tsv.xml @ 4:285060661b45 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv commit 36e9065027cc7bf721e9d203208477ee88906c57"
author iuc
date Thu, 23 Jan 2020 08:00:49 -0500
parents e92b3c0f9224
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e92b3c0f9224 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcf2tsv commit c2af291b241e37e0a55adbc1fc72a9fa37d93582
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1 <tool id="vcf2tsv" name="VCFtoTab-delimited:" version="@WRAPPER_VERSION@+galaxy0">
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2 <description>Convert VCF data into TAB-delimited format</description>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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3 <macros>
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4 <import>macros.xml</import>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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5 </macros>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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6 <expand macro="requirements"/>
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7 <expand macro="stdio" />
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8 <command>vcf2tsv ${g_option} -n '${null_filler}' '${input}' > '${out_file1}'</command>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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9 <inputs>
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10 <param format="vcf" name="input" type="data" label="Select VCF dataset to convert"/>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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11 <param name="g_option" type="boolean" checked="true" truevalue="-g" falsevalue="" label="Report data per sample" help="-g option"/>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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12 <param name="null_filler" type="select" label="Fill empty fields with" help="-n option" >
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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13 <option value="">Nothing</option>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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14 <option value=".">.</option>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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15 <option value="*">*</option>
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16 <option value="NULL">NULL</option>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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17 </param>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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18 </inputs>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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19 <outputs>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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20 <data format="tabular" name="out_file1" />
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 </outputs>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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22 <tests>
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23 <test>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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24 <param name="g_option" value="true"/>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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25 <param name="null_filler" value="."/>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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26 <param name="input" value="vcflib.vcf"/>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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27 <output name="out_file1" file="vcf2tsv-test1.tab"/>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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28 </test>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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29 <test>
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30 <param name="g_option" value="false"/>
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31 <param name="null_filler" value="."/>
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32 <param name="input" value="vcflib.vcf"/>
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33 <output name="out_file1" file="vcf2tsv-test2.tab"/>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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34 </test>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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35 </tests>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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36 <help>
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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37 Converts VCF dataset to tab-delimited format, using null string to replace empty values in the table.
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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38 Specifying "**Report data per sample**" (-g) will output one line per sample with genotype information.
8fb92fcd20ae planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcf2tsv commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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39
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40 ----
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42 Vcf2Tsv @IS_PART_OF_VCFLIB@
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43 </help>
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44 <expand macro="citations" />
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45 </tool>