Mercurial > repos > peterjc > fasta_filter_by_id
comparison tools/fasta_tools/fasta_filter_by_id.xml @ 1:5cd569750e85
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:22:48 -0400 |
parents | 2e5f8ad1a096 |
children | 5b552b3005f2 |
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0:2e5f8ad1a096 | 1:5cd569750e85 |
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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> |