Mercurial > repos > rnateam > rnacommender

annotate rnacommender.xml @ 0:d04fa5201f51 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
author rnateam
date Thu, 28 Jul 2016 05:56:54 -0400
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children 79c9b4b34b63
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d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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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 <command detect_errors="aggressive">
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13 <![CDATA[
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14 sh $__tool_directory__/init.sh 2> hide.txt &&
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15 THEANO_FLAGS=base_compiledir=./tmp python $__tool_directory__/main.py "$infile"
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16 ]]></command>
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17 <inputs>
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18 <param name="infile" type="data" format="fasta" label="Fasta file containing (exactly) one RBP sequence"/>
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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19 </inputs>
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20 <outputs>
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21 <data format="tabular" from_work_dir="output.txt" name="outfile" />
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="infile" value="sample.fa" />
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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26 <output name="outfile">
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27 <assert_contents>
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28 <has_text_matching expression="RBP\ttarget\ty_hat"/>
d04fa5201f51 planemo upload for repository https://github.com/bgruening/galaxytools/tree/rna_commander/tools/rna_tools/rna_commender commit 7ad344d108076116e702e1c1e91cea73d8fcadc4
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29 </assert_contents>
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30 </output>
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31 </test>
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32 </tests>
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33 <help><![CDATA[
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34 RNAcommender 0.1.0 (GALAXY version).
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35 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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36 RNAcommender full package is available at https://github.com/gianlucacorrado/RNAcommender.
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37 ]]></help>
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38 <citations>
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39 <citation type="bibtex">
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40 @ARTICLE{corrado2016rnacommender,
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41 Author = {Gianluca Corrado, Toma Tebaldi, Fabrizio Costa, Paolo Frasconi and Andrea Passerini},
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42 keywords = {machine learning, bioinformatics, post-trainscriptional regulation, gene expression},
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43 title = {{RNAcommender: genome-wide recommendation of RNA-protein interactions.}},
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44 url = {https://github.com/gianlucacorrado/RNAcommender}
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45 }
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46 </citation>
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47 </citations>
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48 </tool>