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annotate extract_transcript_to_gene_map_from_trinity.xml @ 0:e5e836936d60 draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80
author artbio
date Sat, 31 Mar 2018 21:30:07 -0400
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e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80
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1 <tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="0.4.0">
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2 <description>extract transcript to gene map from trinity</description>
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3 <requirements>
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4 <requirement type="package" version="1.3.0">rsem</requirement>
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5 </requirements>
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6 <stdio>
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7 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
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8 </stdio>
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9 <command>
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10 extract-transcript-to-gene-map-from-trinity $trinity_fasta_file $map_file
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11 </command>
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12 <inputs>
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13 <param name="trinity_fasta_file" type="data" format="fasta" label="Trinity fasta file" />
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14 </inputs>
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15 <outputs>
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16 <data format="tabular" name="map_file" label="${tool.name} on ${on_string}: gene map file"/>
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name="trinity_fasta_file" value="trinity_assembled_transcripts.fasta" ftype="fasta"/>
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21 <output name="map_file" file="trinity_gene_map.tabular"/>
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22 </test>
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23 </tests>
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24 <help>
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25
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27 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
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29 NAME
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30 extract-transcript-to-gene-map-from-trinity
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32 SYNOPSIS
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33 extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file
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34
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35 DESCRIPTION
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36 generates a gene_mp_file from a trinity fasta file
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39 </help>
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40 <citations>
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41 <citation type="doi">10.1038/nbt.1883</citation>
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42 </citations>
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43 </tool>