Mercurial > repos > iuc > trinity_gene_to_trans_map

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c6eab3b60743dfa415dc135d657267cc8a0a31ce
author iuc
date Tue, 08 Aug 2023 09:04:29 +0000
parents ba460ccf0006
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ba460ccf0006 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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1 <tool id="trinity_gene_to_trans_map" name="Generate gene to transcript map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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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>
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5 </macros>
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7e3849997c91 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"
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6 <expand macro="bio_tools"/>
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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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7 <expand macro="requirements"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 get_Trinity_gene_to_trans_map.pl '$assembly' > '$map'
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10 ]]></command>
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11 <inputs>
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12 <param format="fasta" name="assembly" type="data" label="Trinity assembly"/>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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13 </inputs>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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14 <outputs>
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15 <data format="tabular" name="map" label="${tool.name} on ${on_string}: Genes to transcripts map"/>
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16 </outputs>
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17 <tests>
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18 <test>
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19 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
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20 <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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21 </test>
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22 </tests>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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23 <help>
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24 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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25 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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26 The output file is intended to be used by the "Align reads and estimate abundance" tool.
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27 The same file is automatically generated when running Trinity, this tool is only intended to be used when you don't (or no longer) have access to the one produced by Trinity.
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29 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
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30 </help>
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31 <expand macro="citation" />
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32 </tool>