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planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ef62aa3d86abd4b911e35447646712a4628e7fe
author rnateam
date Fri, 29 Jul 2016 03:27:18 -0400
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21130153e729 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit d5a6f8df417e899092599e956e8033d502bea3c8
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1 <tool id="rbc_rnacommender" name="RNAcommender" version="0.1.1">
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2 <description>genome-wide recommendation of RNA-protein interactions</description>
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3 <requirements>
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4 <requirement type="package" version="3.5">sam</requirement>
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5 <requirement type="package" version="1.11.1">numpy</requirement>
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6 <requirement type="package" version="0.17.1">scipy</requirement>
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7 <requirement type="package" version="0.18.1">pandas</requirement>
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8 <requirement type="package" version="3.2.2">pytables</requirement>
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9 <requirement type="package" version="0.8.2">theano</requirement>
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10 <requirement type="package" version="2.10.0">requests</requirement>
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11 </requirements>
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12 <stdio>
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13 <exit_code range="1:" />
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14 <exit_code range=":-1" />
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15 <regex match="Error:" />
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16 <regex match="Exception:" />
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17 </stdio>
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18 <command>
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19 <![CDATA[
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20 sh $__tool_directory__/init.sh 2> hide.txt &&
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21 THEANO_FLAGS=base_compiledir=./tmp python $__tool_directory__/main.py "$infile"
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22 ]]></command>
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23 <inputs>
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24 <param name="infile" type="data" format="fasta" label="Fasta file containing (exactly) one RBP sequence"/>
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25 </inputs>
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26 <outputs>
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27 <data format="tabular" from_work_dir="output.txt" name="outfile" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="infile" value="sample.fa" />
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32 <output name="outfile">
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33 <assert_contents>
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34 <has_text_matching expression="RBP\ttarget\ty_hat"/>
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35 </assert_contents>
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36 </output>
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37 </test>
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38 </tests>
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39 <help><![CDATA[
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40 RNAcommender 0.1.0 (GALAXY version).
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41 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.
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42 RNAcommender full package is available at https://github.com/gianlucacorrado/RNAcommender.
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43 ]]></help>
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44 <citations>
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45 <citation type="bibtex">
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46 @ARTICLE{corrado2016rnacommender,
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47 Author = {Gianluca Corrado, Toma Tebaldi, Fabrizio Costa, Paolo Frasconi and Andrea Passerini},
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48 keywords = {machine learning, bioinformatics, post-trainscriptional regulation, gene expression},
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49 title = {{RNAcommender: genome-wide recommendation of RNA-protein interactions.}},
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50 url = {https://github.com/gianlucacorrado/RNAcommender}
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51 }
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52 </citation>
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53 </citations>
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54 </tool>