Mercurial > repos > rnateam > aresite2
comparison aresite2.xml @ 0:6d3269dc319e draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/aresite2 commit f437f5e8c6c856c6f0bb8d8ea6e34f5441ee088f
author | rnateam |
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date | Thu, 02 Feb 2017 19:33:27 -0500 |
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children | a3ce813ed604 |
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1 <tool id="AREsite2_REST" name="Get motifs from AREsite2" version="0.1.2"> | |
2 <description>AREsite2 REST Interface</description> | |
3 <requirements> | |
4 <requirement type="package" version="2.12.4">requests</requirement> | |
5 <requirement type="package" version="1.10.0">six</requirement> | |
6 </requirements> | |
7 <command> | |
8 <![CDATA[ | |
9 python '$__tool_directory__/aresite2.py' | |
10 -g '$gene' | |
11 -m '$motif' | |
12 -s '$species_selector' | |
13 > '$AREsite2_REST_out' | |
14 ]]> | |
15 </command> | |
16 | |
17 <inputs> | |
18 <param name="gene" type="text" label="Gene ID to search for" help="Try e.g. cxcl2" /> | |
19 <param name="species_selector" type="select" label="Select species"> | |
20 <option value="Homo_sapiens" selected="true"></option> | |
21 <option value="Mus_musculus"></option> | |
22 <option value="Danio_rerio"></option> | |
23 <option value="Drosophila_melanogaster"></option> | |
24 <option value="Caenorhabditis_elegans"></option> | |
25 </param> | |
26 <param name="motif" type="text" label="Motif to search for" help="Choose a single motif, e.g. ATTTA" /> | |
27 </inputs> | |
28 | |
29 <outputs> | |
30 <data name="AREsite2_REST_out" label="AREsite2_Rest_${motif}_${gene}_${species_selector}" format="bed" /> | |
31 </outputs> | |
32 | |
33 <tests> | |
34 <test> | |
35 <param name="species" value="Homo_sapiens" /> | |
36 <param name="motif" value="ATTTA" /> | |
37 <param name="gene" value="Cxcl2" /> | |
38 <output name="outputFile" file="AREsite2_Rest_ATTTA_cxcl2_Homo_sapiens.bed" /> | |
39 </test> | |
40 </tests> | |
41 | |
42 <help> | |
43 <![CDATA[ | |
44 **What it does** | |
45 | |
46 Retrieve motif information in BED format from AREsite2 using its REST API. | |
47 | |
48 ]]> | |
49 </help> | |
50 <citations> | |
51 <citation type="doi">10.1093/nar/gkv1238</citation> | |
52 </citations> | |
53 </tool> |