# 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 1286538540 -3600 # Node ID b2906cd2d484a25f80134f432b7c36ed18747bb5 # Parent b0286178f81dfcfbfd03e64b2b4fdb347ee75607 Add -word_size as an advanced argument (ideally would be an optional integer with validation) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -22,6 +22,9 @@ blastn #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): -max_target_seqs $adv_opts.max_hits #end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -72,6 +75,7 @@ blastn <param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /> + <param name="word_size" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'level window linker' --> @@ -82,7 +86,11 @@ blastn <option value="-strand minus">Minus (reverse complement)</option></param><!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + <!-- I'd like word_size to be optional, with minimum 4 for blastn --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."><validator type="in_range" min="0" /></param></when> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -22,6 +22,9 @@ blastp #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): -max_target_seqs $adv_opts.max_hits #end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -66,6 +69,7 @@ blastp <param name="filter_query" type="hidden" value="" /><param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /> + <param name="word_size" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> @@ -81,7 +85,11 @@ blastp <option value="-matrix PAM30">PAM30</option></param><!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + <!-- I'd like word_size to be optional, with minimum 2 for blastp --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param></when> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -22,6 +22,9 @@ tblastx #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): -max_target_seqs $adv_opts.max_hits #end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -63,6 +66,7 @@ tblastx <param name="strand" type="hidden" value="" /><param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /> + <param name="word_size" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> @@ -86,6 +90,10 @@ tblastx <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"><validator type="in_range" min="0" /></param> + <!-- I'd like word_size to be optional, with minimum 2 for tblastx --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -22,6 +22,9 @@ blastx #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): -max_target_seqs $adv_opts.max_hits #end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -63,6 +66,7 @@ blastx <param name="strand" type="hidden" value="" /><param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /> + <param name="word_size" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> @@ -83,7 +87,11 @@ blastx <option value="-matrix PAM30">PAM30</option></param><!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + <!-- I'd like word_size to be optional, with minimum 2 for blastx --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param></when> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -21,6 +21,9 @@ tblastn #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): -max_target_seqs $adv_opts.max_hits #end if +#if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): +-word_size $adv_opts.word_size +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -61,6 +64,7 @@ tblastn <param name="filter_query" type="hidden" value="" /><param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /> + <param name="word_size" type="hidden" value="" /></when><when value="advanced"><!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' --> @@ -76,7 +80,11 @@ tblastn <option value="-matrix PAM30">PAM30</option></param><!-- Why doesn't optional override a validator? I want to accept an empty string OR a non-negative integer --> - <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> + <!-- I'd like word_size to be optional, with minimum 2 for blastp --> + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param></when>