Mercurial > repos > gga > chado_phylogeny_gene_families

annotate phylogeny_gene_families.xml @ 15:2fb03e7fd9a8 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit dc7fe1feecc587f7bc5d09108fbf016b0fd317bc"
author gga
date Mon, 18 Nov 2019 09:55:10 -0500
parents 1383275a8210
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1 <?xml version="1.0"?>
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2 <tool id="phylogeny_gene_families" name="Chado refresh gene families" version="@WRAPPER_VERSION@">
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3 <description>for phylogeny module</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 @START_PSQL@ &&
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11 chakin phylogeny gene_families
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13 #if $family_name:
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14 --family_name '$family_name'
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15 #end if
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17 $nuke
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18
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19 > '$results'
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21 @ZIP_PSQL@
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22 ]]></command>
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23 <inputs>
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24 <expand macro="psql_target"/>
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25 <!-- options -->
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26 <param name="family_name" label="Family Name" argument="--family_name" type="text" help="Restrict to families beginning with given prefix" />
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27 <param name="nuke" label="Nuke" argument="--nuke" type="boolean" truevalue="--nuke" falsevalue="" help="Removes all previous gene families data" />
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28 <expand macro="wait_for"/>
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30 </inputs>
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31 <outputs>
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32 <data format="txt" name="results"/>
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33 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
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34 <filter>psql_target['method'] == "pgtools"</filter>
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35 </data>
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36 </outputs>
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37 <help>
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38 Adds an entry in the featureprop table in a chado database for each family a gene belongs to (for use in https://github.com/legumeinfo/lis_context_viewer/).
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40 @HELP@
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41 </help>
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42 </tool>