Mercurial > repos > iuc > trinity_gene_to_trans_map

annotate gene_to_trans_map.xml @ 12:9267b878862e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 3b8670ad0ce9dd90d6a24429bca131362e56d17d"
author iuc
date Fri, 01 Nov 2019 08:14:06 -0400
parents 1b04880ff362
children 318fd1a0646d
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1b04880ff362 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
iuc
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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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83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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2 <description>for Trinity assembly</description>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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3 <macros>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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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>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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6 <expand macro="requirements"/>
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9502ad75fc87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
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7 <command detect_errors="aggressive"><![CDATA[
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1b04880ff362 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
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8 get_Trinity_gene_to_trans_map.pl '$assembly' > '$map'
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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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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>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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11 <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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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>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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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>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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16 <tests>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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17 <test>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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18 <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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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>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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21 </tests>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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22 <help>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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23 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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24 This tool produces a file containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity.
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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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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26 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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83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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28 .. _Trinity: http://trinityrnaseq.github.io
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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29 </help>
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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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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31 <expand macro="citation" />
83c862e77b99 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214
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32 </tool>