Mercurial > repos > gga > apollo_feat_from_gff3

annotate create_features_from_gff3.xml @ 14:9f9aa5a88972 draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f274d9deece87f6837ffb0a22d9231671be4542"
author gga
date Wed, 19 Aug 2020 06:54:11 -0400
parents bb562d95b6cd
children 250745643de2
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1 <?xml version="1.0"?>
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2 <tool id="feat_from_gff3" name="GFF3 to Apollo Annotations" version="@WRAPPER_VERSION@">
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3 <description></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 <code file="webapollo.py"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @AUTH@
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12 python '$__tool_directory__/create_features_from_gff3.py'
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13 @ORG_OR_GUESS@
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14
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15 '$__user_email__'
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16 '$gff3_data'
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17 --source '${__app__.config.galaxy_infrastructure_url}/history/view/${__app__.security.encode_id($gff3_data.history_id)}'
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18 $use_name
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19 $disable_cds_recalculation
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20
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21 > '$output']]></command>
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22 <inputs>
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23 <expand macro="org_or_guess" />
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24 <expand macro="gff3_input" />
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25 <param name="use_name" type="boolean" truevalue="--user_name" falsevalue="" label="Use the given name instead of generating one" />
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26 <param name="disable_cds_recalculation" type="boolean" truevalue="--disable_cds_recalculation" falsevalue="" label="Disable CDS recalculation and instead use the one provided" />
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27 </inputs>
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28 <outputs>
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29 <data format="txt" name="output" label="Process and Error Log"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <conditional name="org_source">
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34 <param name="source_select" value="direct"/>
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35 <param name="org_raw" value="Test org" />
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36 </conditional>
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37 <param name="gff3_data" value="merlin.gff"/>
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38 <output name="output" file="load_gff3/output.txt" compare="sim_size"/>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 @REFERENCES@
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43 ]]></help>
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44 <expand macro="citations"/>
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45 </tool>