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comparison rnacommender.xml @ 0:8918de535391 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 2fc7f3c08f30e2d81dc4ad19759dfe7ba9b0a3a1
author rnateam
date Tue, 31 May 2016 05:41:03 -0400
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children 21130153e729
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-1:000000000000 0:8918de535391
1 <tool id="rbc_rnacommender" name="RNAcommender" version="0.1.0">
2 <description>files into a collection</description>
3 <requirements>
4 <requirement type="package" version="3.5">sam</requirement>
5 <requirement type="package" version="1.8.1">numpy</requirement>
6 <requirement type="package" version="0.17.1">pandas</requirement>
7 <requirement type="package" version="3.2.2">pytables</requirement>
8 <requirement type="package" version="0.7">theano</requirement>
9 <requirement type="package" version="2.10.0">requests</requirement>
10 </requirements>
11 <command detect_errors="aggressive">
12 <![CDATA[
13 sh $__tool_directory__/init.sh &&
14 python $__tool_directory__/main.py "$infile"
15 ]]></command>
16 <inputs>
17 <param name="infile" type="data" format="fasta" label="Fasta file to split"/>
18 </inputs>
19 <outputs>
20 <data format="tabular" from_work_dir="output.txt" name="outfile" />
21 </outputs>
22 <tests>
23 <test>
24 <param name="infile" value="sample.fa" />
25 <output name="outfile">
26 <assert_contents>
27 <has_text_matching expression="RBP\ttarget\ty_hat"/>
28 </assert_contents>
29 </output>
30 </test>
31 </tests>
32 <help><![CDATA[
33 RNAcommender 0.1.0 (GALAXY version).
34 In order to get the prediction for one (or more) RBPs, insert one fasta file with the protein sequences. The output will contain a ranked list of targets for ALL the proteins in the input file.
35 RNAcommender full package is available at https://github.com/gianlucacorrado/RNAcommender.
36 ]]></help>
37 <citations>
38 <citation type="bibtex">
39 @ARTICLE{corrado2016rnacommender,
40 Author = {Gianluca Corrado, Toma Tebaldi, Fabrizio Costa, Paolo Frasconi and Andrea Passerini},
41 keywords = {machine learning, bioinformatics, post-trainscriptional regulation, gene expression},
42 title = {{RNAcommender: genome-wide recommendation of RNA-protein interactions.}},
43 url = {https://github.com/gianlucacorrado/RNAcommender}
44 }
45 </citation>
46 </citations>
47 </tool>