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comparison ensembl_longest_cds_per_gene.xml @ 2:6cf9f7f6509c draft default tip

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planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ensembl_longest_cds_per_gene commit 651fae48371f845578753052c6fe173e3bb35670
author earlhaminst
date Wed, 15 Mar 2017 20:23:13 -0400
parents a07680f3033a
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1:a07680f3033a 2:6cf9f7f6509c
1 <tool id="ensembl_longest_cds_per_gene" name="Select longest CDS per gene" version="0.0.1"> 1 <tool id="ensembl_longest_cds_per_gene" name="Select longest CDS per gene" version="0.0.2">
2 <description>from Ensembl CDS FASTA</description> 2 <description>from Ensembl CDS FASTA</description>
3 <command detect_errors="exit_code"><![CDATA[ 3 <command detect_errors="exit_code"><![CDATA[
4 python '$__tool_directory__/ensembl_longest_cds_per_gene.py' -f '$input' -o '$output' 4 python '$__tool_directory__/ensembl_longest_cds_per_gene.py' -f '$input' -o '$output'
5 ]]></command> 5 ]]></command>
6 <inputs> 6 <inputs>
20 20
21 The headers of the input CDS FASTA file are expected to be of the following format:: 21 The headers of the input CDS FASTA file are expected to be of the following format::
22 22
23 >ENSMUST00000177965.1 cds chromosome:GRCm38:12:113456720:113456736:-1 gene:ENSMUSG00000094057.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd2-7 description:immunoglobulin heavy diversity 2-7 [Source:MGI Symbol;Acc:MGI:4439866] 23 >ENSMUST00000177965.1 cds chromosome:GRCm38:12:113456720:113456736:-1 gene:ENSMUSG00000094057.1 gene_biotype:IG_D_gene transcript_biotype:IG_D_gene gene_symbol:Ighd2-7 description:immunoglobulin heavy diversity 2-7 [Source:MGI Symbol;Acc:MGI:4439866]
24 24
25 Among the CDS sequences having the same gene identifier (ENSMUSG00000094057 in the example above), the tool will select the one with the longest sequence. The header of the sequences in the output dataset will contain only the transcript id without version (ENSMUST00000177965 in the example above). 25 Among the CDS sequences having the same gene identifier (ENSMUSG00000094057 in the example above), the tool will select the one with the longest sequence.
26 ]]></help> 26 ]]></help>
27 </tool> 27 </tool>