# 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 1286293730 -3600 # Node ID dd7a3707f323bbf38689a24bfcb0b337c3494569 # Parent 1c8a5958c7481e53e862dbdf44d5367b6f3fc271 Add -matrix option to BLASTP, BLASTX, TBLASTN and TBLASTX (doesn't apply to BLASTN) --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -11,6 +11,7 @@ -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.matrix -out $output1 -outfmt $out_format -num_threads 8 @@ -56,10 +57,21 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="matrix" 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="matrix" type="select" label="Scoring matrix"> + <option value="-matrix BLOSUM62">BLOSUM62 (default)</option> + <option value="-matrix BLOSUM90">BLOSUM90</option> + <option value="-matrix BLOSUM80">BLOSUM80</option> + <option value="-matrix BLOSUM50">BLOSUM50</option> + <option value="-matrix BLOSUM45">BLOSUM45</option> + <option value="-matrix PAM250">PAM250</option> + <option value="-matrix PAM70">PAM70</option> + <option value="-matrix PAM30">PAM30</option> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -11,6 +11,7 @@ -evalue $evalue_cutoff $adv_opts.filter_query $adv_opts.strand + $adv_opts.matrix -out $output1 -outfmt $out_format -num_threads 8 @@ -53,6 +54,7 @@ <when value="basic"><param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /> + <param name="matrix" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> @@ -62,6 +64,16 @@ <option value="-strand plus">Plus (forward)</option><option value="-strand minus">Minus (reverse complement)</option></param> + <param name="matrix" type="select" label="Scoring matrix"> + <option value="-matrix BLOSUM62">BLOSUM62 (default)</option> + <option value="-matrix BLOSUM90">BLOSUM90</option> + <option value="-matrix BLOSUM80">BLOSUM80</option> + <option value="-matrix BLOSUM50">BLOSUM50</option> + <option value="-matrix BLOSUM45">BLOSUM45</option> + <option value="-matrix PAM250">PAM250</option> + <option value="-matrix PAM70">PAM70</option> + <option value="-matrix PAM30">PAM30</option> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -11,6 +11,7 @@ -evalue $evalue_cutoff $adv_opts.filter_query $adv_opts.strand + $adv_opts.matrix -out $output1 -outfmt $out_format -num_threads 8 @@ -53,6 +54,7 @@ <when value="basic"><param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /> + <param name="matrix" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> @@ -62,6 +64,16 @@ <option value="-strand plus">Plus (forward)</option><option value="-strand minus">Minus (reverse complement)</option></param> + <param name="matrix" type="select" label="Scoring matrix"> + <option value="-matrix BLOSUM62">BLOSUM62 (default)</option> + <option value="-matrix BLOSUM90">BLOSUM90</option> + <option value="-matrix BLOSUM80">BLOSUM80</option> + <option value="-matrix BLOSUM50">BLOSUM50</option> + <option value="-matrix BLOSUM45">BLOSUM45</option> + <option value="-matrix PAM250">PAM250</option> + <option value="-matrix PAM70">PAM70</option> + <option value="-matrix PAM30">PAM30</option> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -10,6 +10,7 @@ #end if -evalue $evalue_cutoff $adv_opts.filter_query + $adv_opts.matrix -out $output1 -outfmt $out_format -num_threads 8 @@ -51,10 +52,21 @@ </param><when value="basic"><param name="filter_query" type="hidden" value="" /> + <param name="matrix" 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="matrix" type="select" label="Scoring matrix"> + <option value="-matrix BLOSUM62">BLOSUM62 (default)</option> + <option value="-matrix BLOSUM90">BLOSUM90</option> + <option value="-matrix BLOSUM80">BLOSUM80</option> + <option value="-matrix BLOSUM50">BLOSUM50</option> + <option value="-matrix BLOSUM45">BLOSUM45</option> + <option value="-matrix PAM250">PAM250</option> + <option value="-matrix PAM70">PAM70</option> + <option value="-matrix PAM30">PAM30</option> + </param></when></conditional></inputs>