# 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 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)"/>