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annotate extract_transcript_to_gene_map_from_trinity.xml @ 1:f9f98166eff8 draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 153f4b18b27fc78ce2542b07fadd31dd4c23ae4b
author artbio
date Tue, 27 Mar 2018 12:33:39 -0400
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children 39b8e13b1fc9
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8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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1 <tool id="extract_transcript_to_gene_map_from_trinity" name="RSEM trinity fasta to gene map" version="0.1.0">
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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2 <description>extract transcript to gene map from trinity</description>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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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>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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6 <command>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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7 extract-transcript-to-gene-map-from-trinity $trinity_fasta_file $map_file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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8 </command>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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10 <inputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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11 <param name="trinity_fasta_file" type="data" format="fasta" label="Trinity fasta file" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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12 </inputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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13 <stdio>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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14 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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15 </stdio>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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16 <outputs>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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17 <data format="tabular" name="map_file" label="${tool.name} on ${on_string}: gene map file"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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18 </outputs>
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19 <tests>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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20 <test>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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21 <param name="trinity_fasta_file" value="trinity_assembled_transcripts.fasta" ftype="fasta"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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22 <output name="map_file" file="trinity_gene_map.tabular"/>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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23 </test>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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24 </tests>
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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25 <help>
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8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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28 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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30 NAME
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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31 extract-transcript-to-gene-map-from-trinity
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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32
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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33 SYNOPSIS
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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34 extract-transcript-to-gene-map-from-trinity trinity_fasta_file map_file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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36 DESCRIPTION
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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37 generates a gene_mp_file from a trinity fasta file
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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38
8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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8857193bde0e planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit b800e37fa54bbfeb16027133f7c34647ea460419
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40 </help>
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41 </tool>