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Support -db (database) or -subject (FASTA file)

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This commit is contained in:
Peter Cock
2010-10-01 14:37:15 +01:00
parent 1a051f185e
commit ef3d585f47
5 changed files with 125 additions and 44 deletions
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tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
+25 -9
View File
@@ -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 ${db_opts.db_opts_selector}">
<change_format>
<when input="out_format" value="0" format="txt"/>
</change_format>
tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+25 -9
View File
@@ -3,7 +3,11 @@
<command>
blastp
-query "$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 ${db_opts.db_opts_selector}">
<change_format>
<when input="out_format" value="0" format="txt"/>
</change_format>
tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+25 -9
View File
@@ -3,7 +3,11 @@
<command>
blastx
-query "$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 ${db_opts.db_opts_selector}">
<change_format>
<when input="out_format" value="0" format="txt"/>
</change_format>
tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+25 -8
View File
@@ -3,7 +3,11 @@
<command>
tblastn
-query "$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 ${db_opts.db_opts_selector}">
<change_format>
<when input="out_format" value="0" format="txt"/>
</change_format>
tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+25 -9
View File
@@ -3,7 +3,11 @@
<command>
tblastx
-query "$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>