Mercurial > repos > gga > apollo_feat_from_gff3

annotate create_features_from_gff3.xml @ 9:09dacc7c6a21 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 49fe23e3fb330234900946352fbc3a86deeeb639
author gga
date Mon, 29 Jul 2019 10:11:02 -0400
parents cc098732daf6
children 5d1cf95ade8a
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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 python $__tool_directory__/create_features_from_gff3.py
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11 @ADMIN_AUTH@
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12 @ORG_OR_GUESS@
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14 "$__user_email__"
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15 '$gff3_data'
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16 --source "${__app__.config.galaxy_infrastructure_url}history/view/${__app__.security.encode_id($gff3_data.history_id)}"
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18 > $output]]></command>
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19 <inputs>
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20 <expand macro="org_or_guess" />
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21 <expand macro="gff3_input" />
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22 </inputs>
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23 <outputs>
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24 <data format="tabular" name="output" label="Process and Error Log">
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25 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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26 </data>
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27 </outputs>
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28 <tests>
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29 <test expect_failure="true">
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30 <conditional name="org_source">
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31 <param name="source_select" value="direct"/>
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32 <param name="org_raw" value="Test org" />
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33 </conditional>
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34 <param name="gff3_data" value="good-model.gff3"/>
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35 <expand macro="test_result" />
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36 </test>
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37 </tests>
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38 <help><![CDATA[
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39 **NOTA BENE**
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40
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41 This is **incredibly, highly experimental**
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42
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43 DO NOT:
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44
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45 - Run on gff3 referencing multiple reference sequences/contigs
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46 - Expect it to work well
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47 - Expect it to work at all
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48
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49 @REFERENCES@
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50 ]]></help>
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51 <expand macro="citations"/>
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52 </tool>