Mercurial > repos > iuc > trinity_gene_to_trans_map

annotate gene_to_trans_map.xml @ 9:1d65be4c5039 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4
author iuc
date Thu, 14 Jun 2018 03:08:16 -0400
parents aad66a0cda96
children 4dba8ad5c879
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1d65be4c5039 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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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>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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3 <macros>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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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>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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6 <expand macro="requirements"/>
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aad66a0cda96 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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1d65be4c5039 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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1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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9 ]]></command>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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10 <inputs>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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11 <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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12 </inputs>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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13 <outputs>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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14 <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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15 </outputs>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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16 <tests>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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17 <test>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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18 <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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19 <output name="map" file="raw/map.tsv" />
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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20 </test>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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21 </tests>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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22 <help>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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23 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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24 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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25 The output file is intended to be used by the "Align reads and estimate abundance" tool.
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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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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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1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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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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28 .. _Trinity: http://trinityrnaseq.github.io
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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29 </help>
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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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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31 <expand macro="citation" />
1bbdff0c4dba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1599ee1b8e873cf0e40d4a63bb7c734317db4eed
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32 </tool>