Mercurial > repos > gga > chado_phylogeny_gene_order

annotate phylogeny_gene_order.xml @ 14:3d40a4918ffe draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bfca9a8c38694bbf04d92a6668e4ea31cf658eb8"
author gga
date Thu, 14 Nov 2019 10:01:24 -0500
parents 954d702c935e
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1 <?xml version="1.0"?>
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2 <tool id="phylogeny_gene_order" name="Chado gene ordering" 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_order
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13 $nuke
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14
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15 > '$results'
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17 @ZIP_PSQL@
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18 ]]></command>
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19 <inputs>
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20 <expand macro="psql_target"/>
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21 <!-- options -->
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22 <param name="nuke" label="Nuke" argument="--nuke" type="boolean" truevalue="--nuke" falsevalue="" help="Removes all previous gene ordering data" />
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23 <expand macro="wait_for"/>
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25 </inputs>
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26 <outputs>
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27 <data format="txt" name="results"/>
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28 <data format="postgresql" name="outfile" from_work_dir="postgresql_out.tar.bz2" label="${tool.name} on ${on_string}">
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29 <filter>psql_target['method'] == "pgtools"</filter>
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30 </data>
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31 </outputs>
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32 <help>
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33 Orders all the genes in the database by their order on their respective chromosomes in the gene_order table (for use in https://github.com/legumeinfo/lis_context_viewer/).
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35 @HELP@
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36 </help>
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37 </tool>