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