annotate gene_to_trans_map.xml @ 8:c2c039e421af draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
author iuc
date Mon, 22 Jan 2018 11:27:24 -0500
parents 9502ad75fc87
children 1b04880ff362
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83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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1 <tool id="trinity_gene_to_trans_map" name="Generate gene to transcript map" version="@WRAPPER_VERSION@.0">
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2 <description>for Trinity assembly</description>
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3 <macros>
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4 <import>macros.xml</import>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="aggressive"><![CDATA[
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83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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8 get_Trinity_gene_to_trans_map.pl "$assembly" > "$map"
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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9 ]]></command>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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10 <inputs>
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11 <param format="fasta" name="assembly" type="data" label="Trinity assembly"/>
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12 </inputs>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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13 <outputs>
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14 <data format="tabular" name="map" label="${tool.name} on ${on_string}: Genes to transcripts map"/>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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15 </outputs>
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16 <tests>
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17 <test>
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18 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
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19 <output name="map" file="raw/map.tsv" />
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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20 </test>
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21 </tests>
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22 <help>
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23 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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24 This tool produces a file containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity.
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25 The output file is intended to be used by the "Align reads and estimate abundance" tool.
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27 .. _Trinity: http://trinityrnaseq.github.io
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28 </help>
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30 <expand macro="citation" />
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31 </tool>