Mercurial > repos > peterjc > fasta_filter_by_id

comparison tools/fasta_tools/fasta_filter_by_id.xml @ 1:5cd569750e85

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Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author peterjc
date Tue, 07 Jun 2011 17:22:48 -0400
parents 2e5f8ad1a096
children 5b552b3005f2
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0:2e5f8ad1a096 1:5cd569750e85
1 <tool id="fasta_filter_by_id" name="Filter sequences by ID" version="0.0.2"> 1 <tool id="fasta_filter_by_id" name="Filter FASTA by ID" version="0.0.3">
2 <description>from a tabular file</description> 2 <description>from a tabular file</description>
3 <command interpreter="python"> 3 <command interpreter="python">
4 fasta_filter_by_id.py $input_tabular $columns $input_fasta 4 fasta_filter_by_id.py $input_tabular $columns $input_fasta
5 #if $output_choice_cond.output_choice=="both" 5 #if $output_choice_cond.output_choice=="both"
6 $output_pos $output_neg 6 $output_pos $output_neg
71 single output file of just the matching records, or just the non-matching ones. 71 single output file of just the matching records, or just the non-matching ones.
72 72
73 Note that the order of sequences in the original FASTA file is preserved. 73 Note that the order of sequences in the original FASTA file is preserved.
74 Also, if any sequences share an identifier, duplicates are not removed. 74 Also, if any sequences share an identifier, duplicates are not removed.
75 75
76 **Example Usage**
77
78 Given a FASTA file of proteins you might run a signal peptide search (e.g.
79 via the SignalP wrapper for Galaxy), then filtered these tabular results to
80 select just those with a signal peptide. You could then use this tool to get
81 a FASTA file of only the proteins with predicted signal peptides.
82
76 </help> 83 </help>
77 </tool> 84 </tool>