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galaxy-dist commit d8da4f7bb0f5: Add -ungapped for blastn and blastx (having trouble with blastp and tblastn, not in tblastx)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286554738 -3600 # Node ID d8da4f7bb0f5e1d43b371e4e52fb688ad816e5bf # Parent 8979b429d7691f4121afb368a05e6b9d0ea40706 Add -ungapped for blastn and blastx (having trouble with blastp and tblastn, not in tblastx) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -25,6 +25,7 @@ blastn #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +$adv_opts.ungapped </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -76,6 +77,7 @@ blastn <param name="strand" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /><param name="word_size" type="hidden" value="" /> + <param name="ungapped" type="hidden" value="" /></when><when value="advanced"> @@ -93,6 +95,7 @@ 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> + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -25,6 +25,8 @@ blastp #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +##Ungapped disabled for now - see comments below +##$adv_opts.ungapped </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -70,6 +72,10 @@ blastp <param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /><param name="word_size" type="hidden" value="" /> + </when><when value="advanced"> @@ -92,6 +98,12 @@ 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></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -25,6 +25,7 @@ blastx #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +$adv_opts.ungapped </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -67,6 +68,7 @@ blastx <param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /><param name="word_size" type="hidden" value="" /> + <param name="ungapped" type="hidden" value="" /></when><when value="advanced"> @@ -94,6 +96,7 @@ 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> + <param name="ungapped" type="boolean" label="Perform ungapped alignment only?" truevalue="-ungapped" falsevalue="" checked="false" /></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -24,6 +24,8 @@ tblastn #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0): -word_size $adv_opts.word_size #end if +##Ungapped disabled for now - see comments below +##$adv_opts.ungapped </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -65,6 +67,10 @@ tblastn <param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /><param name="word_size" type="hidden" value="" /> + </when><when value="advanced"> @@ -87,6 +93,12 @@ tblastn <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>

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galaxy-dist commit dd7a3707f323: Add -matrix option to BLASTP, BLASTX, TBLASTN and TBLASTX (doesn't apply to BLASTN)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)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"><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"> @@ -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"> @@ -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"><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>

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galaxy-dist commit b2906cd2d484: Add -word_size as an advanced argument (ideally would be an optional integer with validation)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)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 $adv_opts.word_size +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -72,6 +75,7 @@ blastn <param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /> + <param name="word_size" type="hidden" value="" /></when><when value="advanced"> @@ -82,7 +86,11 @@ blastn <option value="-strand minus">Minus (reverse complement)</option></param> - <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> +  + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 4."><validator type="in_range" min="0" /></param></when> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -22,6 +22,9 @@ blastp #if (str($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 $adv_opts.word_size +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -66,6 +69,7 @@ blastp <param name="filter_query" type="hidden" value="" /><param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /> + <param name="word_size" type="hidden" value="" /></when><when value="advanced"> @@ -81,7 +85,11 @@ blastp <option value="-matrix PAM30">PAM30</option></param> - <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> +  + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param></when> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -22,6 +22,9 @@ tblastx #if (str($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 $adv_opts.word_size +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -63,6 +66,7 @@ tblastx <param name="strand" type="hidden" value="" /><param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /> + <param name="word_size" type="hidden" value="" /></when><when value="advanced"> @@ -86,6 +90,10 @@ tblastx <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"><validator type="in_range" min="0" /></param> +  + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -22,6 +22,9 @@ blastx #if (str($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 $adv_opts.word_size +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -63,6 +66,7 @@ blastx <param name="strand" type="hidden" value="" /><param name="matrix" type="hidden" value="" /><param name="max_hits" type="hidden" value="" /> + <param name="word_size" type="hidden" value="" /></when><when value="advanced"> @@ -83,7 +87,11 @@ blastx <option value="-matrix PAM30">PAM30</option></param> - <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <param name="max_hits" type="integer" value="0" label="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param> +  + <param name="word_size" type="integer" value="0" label="Word size for wordfinder algorithm" help="Use zero for default, otherwise minimum 2."><validator type="in_range" min="0" /></param></when> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -21,6 +21,9 @@ tblastn #if (str($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"> @@ -76,7 +80,11 @@ tblastn <option value="-matrix PAM30">PAM30</option></param> - <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> +  + <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>

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galaxy-dist commit 9bf65ebafa8f: Reduce whitespace in <command> tag (there are OS limits on command line length)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286366018 -3600 # Node ID 9bf65ebafa8fc89115a5b42ebb9865ed99c1cf84 # Parent 6273161e76c33f807145d9b12eafa0a6e414bbf1 Reduce whitespace in <command> tag (there are OS limits on command line length) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -1,20 +1,21 @@ <tool id="ncbi_blastn_wrapper" name="NCBI BLAST+ blastn" version="0.0.1"><description>Search nucleotide database with nucleotide query sequence(s)</description><command> - blastn - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastn -query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -task $blast_type - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.strand - -out $output1 - -outfmt $out_format - -num_threads 8 +-task $blast_type +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.strand +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -1,20 +1,22 @@ <tool id="ncbi_blastp_wrapper" name="NCBI BLAST+ blastp" version="0.0.1"><description>Search protein database with protein query sequence(s)</description><command> - blastp - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastp +-query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -task $blast_type - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.matrix - -out $output1 - -outfmt $out_format - -num_threads 8 +-task $blast_type +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.matrix +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -1,20 +1,22 @@ <tool id="ncbi_tblastx_wrapper" name="NCBI BLAST+ tblastx" version="0.0.1"><description>Search translated nucleotide database with translated nucleotide query sequence(s)</description><command> - tblastx - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +tblastx +-query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.strand - $adv_opts.matrix - -out $output1 - -outfmt $out_format - -num_threads 8 +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.strand +$adv_opts.matrix +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -1,20 +1,22 @@ <tool id="ncbi_blastx_wrapper" name="NCBI BLAST+ blastx" version="0.0.1"><description>Search protein database with translated nucleotide query sequence(s)</description><command> - blastx - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +blastx +-query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.strand - $adv_opts.matrix - -out $output1 - -outfmt $out_format - -num_threads 8 +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.strand +$adv_opts.matrix +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -1,19 +1,21 @@ <tool id="ncbi_tblastn_wrapper" name="NCBI BLAST+ tblastn" version="0.0.1"><description>Search translated nucleotide database with protein query sequence(s)</description><command> - tblastn - -query "$query" +## The command is a Cheetah template which allows some Python based syntax. +## Lines starting hash hash are comments. Galaxy will turn newlines into spaces +tblastn +-query "$query" #if $db_opts.db_opts_selector == "db": - -db "$db_opts.database" + -db "$db_opts.database" #else: - -subject "$db_opts.subject" + -subject "$db_opts.subject" #end if - -evalue $evalue_cutoff - $adv_opts.filter_query - $adv_opts.matrix - -out $output1 - -outfmt $out_format - -num_threads 8 +-evalue $evalue_cutoff +$adv_opts.filter_query +$adv_opts.matrix +-out $output1 +-outfmt $out_format +-num_threads 8 </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/>

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galaxy-dist commit 1c8a5958c748: Use dropdown (default) rather than radio for BLAST databases as could be lots of them
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285945041 -3600 # Node ID 1c8a5958c7481e53e862dbdf44d5367b6f3fc271 # Parent 477eb3cceae79d93be845a8540572033f208ae73 Use dropdown (default) rather than radio for BLAST databases as could be lots of them --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -24,7 +24,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <param name="database" type="select" label="Nucleotide BLAST database"><options from_file="blastdb.loc"><column name="name" index="0"/><column name="value" index="1"/> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -23,7 +23,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Protein BLAST database"> + <param name="database" type="select" label="Protein BLAST database"><options from_file="blastdb_p.loc"><column name="name" index="0"/><column name="value" index="1"/> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -23,7 +23,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <param name="database" type="select" label="Nucleotide BLAST database"><options from_file="blastdb.loc"><column name="name" index="0"/><column name="value" index="1"/> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -23,7 +23,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Protein BLAST database"> + <param name="database" type="select" label="Protein BLAST database"><options from_file="blastdb_p.loc"><column name="name" index="0"/><column name="value" index="1"/> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -22,7 +22,7 @@ <option value="file">FASTA file</option></param><when value="db"> - <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <param name="database" type="select" label="Nucleotide BLAST database"><options from_file="blastdb.loc"><column name="name" index="0"/><column name="value" index="1"/>

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galaxy-dist commit 6273161e76c3: Make BLOSUM62 the default with sensible sorting (tip from Ross Lazarus on mailing list)
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286293953 -3600 # Node ID 6273161e76c33f807145d9b12eafa0a6e414bbf1 # Parent dd7a3707f323bbf38689a24bfcb0b337c3494569 Make BLOSUM62 the default with sensible sorting (tip from Ross Lazarus on mailing list) --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -63,9 +63,9 @@ <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 BLOSUM62" selected="true">BLOSUM62 (default)</option><option value="-matrix BLOSUM50">BLOSUM50</option><option value="-matrix BLOSUM45">BLOSUM45</option><option value="-matrix PAM250">PAM250</option> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -65,9 +65,9 @@ <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 BLOSUM62" selected="true">BLOSUM62 (default)</option><option value="-matrix BLOSUM50">BLOSUM50</option><option value="-matrix BLOSUM45">BLOSUM45</option><option value="-matrix PAM250">PAM250</option> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -65,15 +65,16 @@ <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 BLOSUM62" selected="true">BLOSUM62 (default)</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 @@ -58,9 +58,9 @@ <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 BLOSUM62" selected="true">BLOSUM62 (default)</option><option value="-matrix BLOSUM50">BLOSUM50</option><option value="-matrix BLOSUM45">BLOSUM45</option><option value="-matrix PAM250">PAM250</option>

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galaxy-dist commit f5f74df868f1: Comment out blastn vecscreen as not supported
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286381298 -3600 # Node ID f5f74df868f1dfb369ec723ef2cb9f0926eaa760 # Parent c4c2b6eea3e11ee8a024b32f58419f7b1d36f114 Comment out blastn vecscreen as not supported --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -49,7 +49,10 @@ blastn <option value="blastn">blastn</option><option value="blastn-short">blastn-short</option><option value="dc-megablast">dc-megablast</option> + </param><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /><param name="out_format" type="select" label="Output format">

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galaxy-dist commit b0286178f81d: Fixed silly typo
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286383905 -3600 # Node ID b0286178f81dfcfbfd03e64b2b4fdb347ee75607 # Parent f5f74df868f1dfb369ec723ef2cb9f0926eaa760 Fixed silly typo --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -83,7 +83,7 @@ tblastx <option value="-matrix PAM30">PAM30</option></param> - <param name="max_hits" type="integer" value="0" lable="Maximum hits to show (in plain text output)" 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></when>

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galaxy-dist commit 477eb3cceae7: Updated a caption for consistency, removed an old comment
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1285944657 -3600 # Node ID 477eb3cceae79d93be845a8540572033f208ae73 # Parent 36086d5bd8fa174ce88443eeeefec52b8fada5bd Updated a caption for consistency, removed an old comment --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -33,7 +33,7 @@ </when><when value="file"><param name="database" type="hidden" value="" /> - <param name="subject" type="data" format="fasta" label="Protein subject sequence(s)"/> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/></when></conditional><param name="evalue_cutoff" type="float" size="15" value="0.001" label="set expectation value cutoff" /> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -59,7 +59,6 @@ </conditional></inputs><outputs> - <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/>

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galaxy-dist commit c4c2b6eea3e1: Added support for BLAST+ -max_target_seqs option
by commits-noreply＠bitbucket.org 20 Nov '10

20 Nov '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User peterjc <p.j.a.cock(a)googlemail.com> # Date 1286381268 -3600 # Node ID c4c2b6eea3e11ee8a024b32f58419f7b1d36f114 # Parent 9bf65ebafa8fc89115a5b42ebb9865ed99c1cf84 Added support for BLAST+ -max_target_seqs option --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -3,7 +3,8 @@ <command> ## The command is a Cheetah template which allows some Python based syntax. ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces -blastn -query "$query" +blastn +-query "$query" #if $db_opts.db_opts_selector == "db": -db "$db_opts.database" #else: @@ -16,6 +17,11 @@ blastn -query "$query" -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -62,6 +68,7 @@ blastn -query "$query" <when value="basic"><param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -71,6 +78,10 @@ blastn -query "$query" <option value="-strand plus">Plus (forward)</option><option value="-strand minus">Minus (reverse complement)</option></param> +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -17,6 +17,11 @@ blastp -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -60,6 +65,7 @@ blastp <when value="basic"><param name="filter_query" type="hidden" value="" /><param name="matrix" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -74,6 +80,10 @@ blastp <option value="-matrix PAM70">PAM70</option><option value="-matrix PAM30">PAM30</option></param> +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -17,6 +17,11 @@ tblastx -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -57,6 +62,7 @@ tblastx <param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /><param name="matrix" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -76,6 +82,10 @@ tblastx <option value="-matrix PAM70">PAM70</option><option value="-matrix PAM30">PAM30</option></param> +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show (in plain text output)" help="Use zero for default limits"> + <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 @@ -17,6 +17,11 @@ blastx -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> @@ -57,6 +62,7 @@ blastx <param name="filter_query" type="hidden" value="" /><param name="strand" type="hidden" value="" /><param name="matrix" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -76,7 +82,10 @@ blastx <option value="-matrix PAM70">PAM70</option><option value="-matrix PAM30">PAM30</option></param> - +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -16,6 +16,11 @@ tblastn -out $output1 -outfmt $out_format -num_threads 8 +## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string +## Note -max_target_seqs overrides -num_descriptions and -num_alignments +#if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0): +-max_target_seqs $adv_opts.max_hits +#end if </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> @@ -55,6 +60,7 @@ tblastn <when value="basic"><param name="filter_query" type="hidden" value="" /><param name="matrix" type="hidden" value="" /> + <param name="max_hits" type="hidden" value="" /></when><when value="advanced"> @@ -69,6 +75,10 @@ tblastn <option value="-matrix PAM70">PAM70</option><option value="-matrix PAM30">PAM30</option></param> +  + <param name="max_hits" type="integer" value="0" lable="Maximum hits to show" help="Use zero for default limits"> + <validator type="in_range" min="0" /> + </param></when></conditional></inputs>

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