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annotate export.xml @ 5:950fb2bf116d draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
author gga
date Fri, 31 Aug 2018 09:33:38 -0400
parents 5559e41721c3
children f45ad96c9e08
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1 <?xml version="1.0"?>
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2 <tool id="export" name="Retrieve Data" version="3.1">
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3 <description>from Apollo into Galaxy</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 $__tool_directory__/export.py
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12 @ADMIN_AUTH@
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14 @ORG_CN_OR_GUESS@
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16 --gff "$gff_out"
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17 --fasta "$fasta_out"
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18 --json "$json_out"
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19
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20 "$__user_email__"
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21
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22 ]]></command>
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23 <inputs>
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24 <expand macro="cn_or_guess" />
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25 </inputs>
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26 <outputs>
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27 <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
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28 <data format="fasta" name="fasta_out" label="Sequence(s) from Apollo"/>
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29 <data format="json" name="json_out" label="Metadata from Apollo">
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30 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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31 </data>
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32 </outputs>
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33 <tests>
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34 <test expect_failure="true">
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35 <conditional name="org_source">
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36 <param name="source_select" value="direct"/>
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37 <param name="org_raw" value="Test org" />
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38 </conditional>
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39 <conditional name="cn_source">
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40 <param name="source_select" value="all"/>
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41 </conditional>
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42 <expand macro="test_result" />
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43 </test>
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44 </tests>
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45 <help><![CDATA[
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46 **What it does**
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47
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48 Exports the sequence data and annotations from Apollo.
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49
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50 If you provide an Apollo JSON file as input to the Organism Common Name list,
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51 this will enable extracting multiple organism's data at once from Apollo.
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52 Beware that currently all gff3 and fasta responses are merged together. If you
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53 have two separate organisms with identically named reference sequences, it will
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54 not be possible to separate those out.
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55
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56 @REFERENCES@
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57 ]]></help>
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58 <expand macro="citations"/>
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59 </tool>