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annotate cravat_submit.xml @ 0:83181dabeb90 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
author galaxyp
date Fri, 18 May 2018 13:25:29 -0400
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83181dabeb90 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3
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1 <tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0">
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2 <description>Submits, checks for, and retrieves data for cancer annotation</description>
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3 <command interpreter="python">cravat_submit.py $input $dropdown $GRCh $psm $Variant $Gene $Noncoding $Error</command>
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6 <inputs>
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8 <param format="tabular" name="input" type="data" label="Source file"> </param>
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9 <param format="tabular" name="dropdown" type="select" label="Analysis Program">
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10 <option value="">None</option>
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11 <option value="VEST">VEST</option>
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12 <option value="CHASM">CHASM</option>
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13 <option value="VEST;CHASM">VEST and CHASM</option>
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14 </param>
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15 <param format="tabular" name="GRCh" type="select" label="Genome Reference Consortium Human Build (GRCh)">
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16 <option value="GRCh38">GRCh38/hg38</option>
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17 <option value="GRCh37">GRCh37/hg19</option>
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18 </param>
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19 <param format="tabular" name="psm" type="data" optional="true" label="ProBED File(Optional)"> </param>
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22 </inputs>
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24 <outputs>
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25 <collection name="collection" type="list" label="CRAVAT Results: ${on_string} using ${dropdown}">
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26 <data format="cravat" label="CRAVAT: Gene Level Annotation Report" name="Gene" />
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27 <data format="cravat" label="CRAVAT: Variant Report" name="Variant" />
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28 <data format="cravat" label="CRAVAT: Non-coding Variant Report" name="Noncoding" />
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29 <data format="cravat" label="CRAVAT: Errors" name="Error" />
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30 </collection>
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31 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input" value="fa_gc_content_input.fa"/>
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36 <output name="out_file1" file="fa_gc_content_output.txt"/>
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37 </test>
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38 </tests>
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40 <help>
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41 This tool submits, checks for, and retrieves data for cancer annotation from the CRAVAT platform at cravat.us.
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42 </help>
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44 </tool>