Mercurial > repos > gga > apollo_feat_from_gff3

annotate create_features_from_gff3.xml @ 10:5d1cf95ade8a draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:51:05 -0500
parents 09dacc7c6a21
children bb562d95b6cd
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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 '$__tool_directory__/create_features_from_gff3.py'
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13 @ORG_OR_GUESS@
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15 '$__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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19 > '$output']]></command>
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20 <inputs>
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21 <expand macro="org_or_guess" />
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22 <expand macro="gff3_input" />
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23 </inputs>
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24 <outputs>
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25 <data format="tabular" name="output" label="Process and Error Log">
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26 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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27 </data>
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28 </outputs>
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29 <tests>
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30 <test>
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31 <conditional name="org_source">
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32 <param name="source_select" value="direct"/>
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33 <param name="org_raw" value="Test org" />
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34 </conditional>
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35 <param name="gff3_data" value="merlin.gff"/>
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36 <output name="output" file="load_gff3/output.tsv" compare="sim_size"/>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 **NOTA BENE**
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42 This is **incredibly, highly experimental**
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44 DO NOT:
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46 - Run on gff3 referencing multiple reference sequences/contigs
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47 - Expect it to work well
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48 - Expect it to work at all
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49
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50 @REFERENCES@
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51 ]]></help>
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52 <expand macro="citations"/>
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53 </tool>