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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 08:52:04 +0000
parents 78b742ff461b
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78b742ff461b 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>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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3 <macros>
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4 <import>macros.xml</import>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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5 </macros>
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9066ddf7a18b "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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1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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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>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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11 <inputs>
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12 <param format="fasta" name="assembly" type="data" label="Trinity assembly"/>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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13 </inputs>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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14 <outputs>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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15 <data format="tabular" name="map" label="${tool.name} on ${on_string}: Genes to transcripts map"/>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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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"/>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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20 <output name="map" file="raw/map.tsv" />
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21 </test>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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22 </tests>
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23 <help>
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24 Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
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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>