# 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 1285931141 -3600 # Node ID 5176fa11ef2f45df4a7bb0b82f2ca0871aaf2465 # Parent 6c1d520f25d44f80de926285cbd927bc35f69a6a Add -strand as adv opt to blastn, blastx and tblastx wrappers --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -7,6 +7,7 @@ -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.strand -out $output1 -outfmt $out_format -num_threads 8 @@ -42,10 +43,16 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="strand" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --><param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -6,6 +6,7 @@ -db "$database" -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.strand -out $output1 -outfmt $out_format -num_threads 8 @@ -34,10 +35,16 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="strand" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -6,6 +6,7 @@ -db "$database" -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.strand -out $output1 -outfmt $out_format -num_threads 8 @@ -34,10 +35,16 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="strand" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --><param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /> + <param name="strand" type="select" label="Query strand(s) to search against database/subject"> + <option value="-strand both">Both</option> + <option value="-strand plus">Plus (forward)</option> + <option value="-strand minus">Minus (reverse complement)</option> + </param></when></conditional></inputs>