Mercurial > repos > iuc > trinity_gene_to_trans_map

annotate gene_to_trans_map.xml @ 16:4dba8ad5c879 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
author iuc
date Fri, 10 Sep 2021 22:35:17 +0000
parents 1d65be4c5039
children 9066ddf7a18b
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1d65be4c5039 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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1 <tool id="trinity_gene_to_trans_map" name="Generate gene to transcript map" version="@WRAPPER_VERSION@">
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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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2 <description>for Trinity assembly</description>
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4dba8ad5c879 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 33aaad8d6afce20732d8232fbcd777a3aabf09ec"
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3 <expand macro="bio_tools"/>
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4 <macros>
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5 <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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6 </macros>
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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>
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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.
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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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.
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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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: http://trinityrnaseq.github.io
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30 </help>
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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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32 <expand macro="citation" />
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33 </tool>