# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock@googlemail.com> # Date 1285929247 -3600 # Node ID aa7f4bdc2eab6be57fc1311137ce423eb39750cd # Parent 55f909b601c49dc0bb53f4fee538605df04d19f4 Use a select parameter for picking just column 1 or 2. Less flexible but works better for BLAST output I think --- a/tools/ncbi_blast_plus/blast_filter_fasta.xml +++ b/tools/ncbi_blast_plus/blast_filter_fasta.xml @@ -1,12 +1,15 @@ -<tool id="blast_filter_fasta" name="BLAST filter FASTA file" version="0.0.1"> +<tool id="blast_filter_fasta" name="Filter FASTA using BLAST output" version="0.0.1"><description>Divide a FASTA file based on BLAST hits</description><command interpreter="python"> blast_filter_fasta.py $blast_file $blast_col $in_file $out_positive_file $out_negative_file </command><inputs> + <param name="in_file" type="data" format="fasta" label="FASTA file to filter"/><param name="blast_file" type="data" format="tabular" label="Tabular BLAST output"/> - <param name="blast_col" type="data_column" data_ref="blast_file" numerical="true" value="1" label="Column containing FASTA identifiers" /> - <param name="in_file" type="data" format="fasta" label="BLAST query FASTA file"/> + <param name="blast_col" type="select" label="Column containing FASTA identifiers"> + <option value="1">Column 1 - BLAST query ID</option> + <option value="2">Column 2 - BLAST match ID</option> + </param></inputs><outputs><data name="out_positive_file" format="fasta" label="Sequences with BLAST hits" /> @@ -21,11 +24,14 @@ **What it does** Typical use would be to take a multi-sequence FASTA and the tabular output of -running BLAST on it, and divides the FASTA file in two: those sequence with a +running BLAST on it, and divide the FASTA file in two: those sequence with a BLAST hit, and those without. In the default NCBI BLAST+ tabular output, the query sequence ID is in column one, and the ID of the match from the database is in column two. +This allows you to filter the FASTA file for the subjects in the BLAST search, +rather than filtering the FASTA file for the queries in the BLAST search. + </help></tool>