Mercurial > repos > rnateam > aresite2

annotate aresite2.xml @ 0:6d3269dc319e draft

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