# 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 1285930037 -3600 # Node ID 6c1d520f25d44f80de926285cbd927bc35f69a6a # Parent aa7f4bdc2eab6be57fc1311137ce423eb39750cd Don't default to setting seg/dust explicitly (allow BLAST+ to use its own defaults) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -6,7 +6,7 @@ -db "$database" -task $blast_type -evalue $evalue_cutoff - -dust $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -41,10 +41,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="yes" falsevalue="no" checked="true" /> + <!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -6,7 +6,7 @@ -db "$database" -task $blast_type -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -38,10 +38,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -5,7 +5,7 @@ -query "$query" -db "$database" -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -33,10 +33,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -5,7 +5,7 @@ -query "$query" -db "$database" -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -33,10 +33,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> + <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> + <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -5,7 +5,7 @@ -query "$query" -db "$database" -evalue $evalue_cutoff - -seg $adv_opts.filter_query + $adv_opts.filter_query -out $output1 -outfmt $out_format -num_threads 8 @@ -33,10 +33,11 @@ <option value="advanced">Show Advanced Options</option></param><when value="basic"> - <param name="filter_query" type="hidden" value="yes" /> + <param name="filter_query" type="hidden" value="" /></when><when value="advanced"> - <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" /> + <!-- 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" /></when></conditional></inputs>