# 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 1285940235 -3600 # Node ID 36086d5bd8fa174ce88443eeeefec52b8fada5bd # Parent 5176fa11ef2f45df4a7bb0b82f2ca0871aaf2465 Support -db (database) or -subject (FASTA file) --- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml @@ -3,7 +3,11 @@ <command> blastn -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query @@ -14,12 +18,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional><param name="blast_type" type="select" display="radio" label="Type of BLAST"><option value="megablast">megablast</option><option value="blastn">blastn</option> @@ -57,8 +74,7 @@ </conditional></inputs><outputs> - <!-- TODO, can I get the caption rather than the value? e.g. 'NT' rather than a long path? --> - <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml @@ -3,7 +3,11 @@ <command> blastp -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -task $blast_type -evalue $evalue_cutoff $adv_opts.filter_query @@ -13,12 +17,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <param name="database" type="select" display="radio" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein FASTA file to use as database"/> + </when> + </conditional><param name="blast_type" type="select" display="radio" label="Type of BLAST"><option value="blastp">blastp</option><option value="blastp-short">blastp-short</option> @@ -47,8 +64,7 @@ </conditional></inputs><outputs> - <!-- TODO, can I get the caption rather than the value? e.g. 'NR' rather than a long path? --> - <data name="output1" format="tabular" label="${blast_type.value_label} on ${database.value_label}"> + <data name="output1" format="tabular" label="${blast_type.value_label} on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml @@ -3,7 +3,11 @@ <command> tblastx -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -evalue $evalue_cutoff $adv_opts.filter_query $adv_opts.strand @@ -13,12 +17,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional><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"><option value="6">Tabular</option> @@ -49,8 +66,7 @@ </conditional></inputs><outputs> - <!-- TODO, can I get the caption rather than the value? e.g. 'NT' rather than a long path? --> - <data name="output1" format="tabular" label="tblastx on ${database.value_label}"> + <data name="output1" format="tabular" label="tblastx on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml @@ -3,7 +3,11 @@ <command> blastx -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -evalue $evalue_cutoff $adv_opts.filter_query $adv_opts.strand @@ -13,12 +17,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> - <param name="database" type="select" display="radio" label="Protein BLAST database"> - <options from_file="blastdb_p.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Protein BLAST database"> + <options from_file="blastdb_p.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Protein subject sequence(s)"/> + </when> + </conditional><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"><option value="6">Tabular</option> @@ -49,8 +66,7 @@ </conditional></inputs><outputs> - <!-- TODO, can I get the caption rather than the value? e.g. 'NR' rather than a long path? --> - <data name="output1" format="tabular" label="blastx on ${database.value_label}"> + <data name="output1" format="tabular" label="blastx on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format> --- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml +++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml @@ -3,7 +3,11 @@ <command> tblastn -query "$query" - -db "$database" +#if $db_opts.db_opts_selector == "db": + -db "$db_opts.database" +#else: + -subject "$db_opts.subject" +#end if -evalue $evalue_cutoff $adv_opts.filter_query -out $output1 @@ -12,12 +16,25 @@ </command><inputs><param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> - <param name="database" type="select" display="radio" label="Nucelotide BLAST database"> - <options from_file="blastdb.loc"> - <column name="name" index="0"/> - <column name="value" index="1"/> - </options> - </param> + <conditional name="db_opts"> + <param name="db_opts_selector" type="select" label="Subject database/sequences"> + <option value="db" selected="True">BLAST Database</option> + <option value="file">FASTA file</option> + </param> + <when value="db"> + <param name="database" type="select" display="radio" label="Nucleotide BLAST database"> + <options from_file="blastdb.loc"> + <column name="name" index="0"/> + <column name="value" index="1"/> + </options> + </param> + <param name="subject" type="hidden" value="" /> + </when> + <when value="file"> + <param name="database" type="hidden" value="" /> + <param name="subject" type="data" format="fasta" label="Nucleotide FASTA file to use as database"/> + </when> + </conditional><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"><option value="6">Tabular</option> @@ -43,7 +60,7 @@ </inputs><outputs><!-- TODO, can I get the caption rather than the value? e.g. 'NT' rather than a long path? --> - <data name="output1" format="tabular" label="tblastn on ${database.value_label}"> + <data name="output1" format="tabular" label="tblastn on ${db_opts.db_opts_selector}"><change_format><when input="out_format" value="0" format="txt"/></change_format>