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comparison 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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1 <tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0">
2 <description>Submits, checks for, and retrieves data for cancer annotation</description>
3 <command interpreter="python">cravat_submit.py $input $dropdown $GRCh $psm $Variant $Gene $Noncoding $Error</command>
4
5
6 <inputs>
7
8 <param format="tabular" name="input" type="data" label="Source file"> </param>
9 <param format="tabular" name="dropdown" type="select" label="Analysis Program">
10 <option value="">None</option>
11 <option value="VEST">VEST</option>
12 <option value="CHASM">CHASM</option>
13 <option value="VEST;CHASM">VEST and CHASM</option>
14 </param>
15 <param format="tabular" name="GRCh" type="select" label="Genome Reference Consortium Human Build (GRCh)">
16 <option value="GRCh38">GRCh38/hg38</option>
17 <option value="GRCh37">GRCh37/hg19</option>
18 </param>
19 <param format="tabular" name="psm" type="data" optional="true" label="ProBED File(Optional)"> </param>
20
21
22 </inputs>
23
24 <outputs>
25 <collection name="collection" type="list" label="CRAVAT Results: ${on_string} using ${dropdown}">
26 <data format="cravat" label="CRAVAT: Gene Level Annotation Report" name="Gene" />
27 <data format="cravat" label="CRAVAT: Variant Report" name="Variant" />
28 <data format="cravat" label="CRAVAT: Non-coding Variant Report" name="Noncoding" />
29 <data format="cravat" label="CRAVAT: Errors" name="Error" />
30 </collection>
31 </outputs>
32
33 <tests>
34 <test>
35 <param name="input" value="fa_gc_content_input.fa"/>
36 <output name="out_file1" file="fa_gc_content_output.txt"/>
37 </test>
38 </tests>
39
40 <help>
41 This tool submits, checks for, and retrieves data for cancer annotation from the CRAVAT platform at cravat.us.
42 </help>
43
44 </tool>