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Add -strand as adv opt to blastn, blastx and tblastx wrappers

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This commit is contained in:
Peter Cock
2010-10-01 12:05:41 +01:00
parent 77fcdf4f4b
commit 1a051f185e
3 changed files with 21 additions and 0 deletions
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tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
+7
View File
@@ -7,6 +7,7 @@
-task $blast_type
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.strand
-out $output1
-outfmt $out_format
-num_threads 8
@@ -42,10 +43,16 @@
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="strand" type="hidden" value="" />
</when>
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
<param name="strand" type="select" label="Query strand(s) to search against database/subject">
<option value="-strand both">Both</option>
<option value="-strand plus">Plus (forward)</option>
<option value="-strand minus">Minus (reverse complement)</option>
</param>
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+7
View File
@@ -6,6 +6,7 @@
-db "$database"
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.strand
-out $output1
-outfmt $out_format
-num_threads 8
@@ -34,10 +35,16 @@
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="strand" type="hidden" value="" />
</when>
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
<param name="strand" type="select" label="Query strand(s) to search against database/subject">
<option value="-strand both">Both</option>
<option value="-strand plus">Plus (forward)</option>
<option value="-strand minus">Minus (reverse complement)</option>
</param>
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+7
View File
@@ -6,6 +6,7 @@
-db "$database"
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.strand
-out $output1
-outfmt $out_format
-num_threads 8
@@ -34,10 +35,16 @@
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="strand" type="hidden" value="" />
</when>
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
<param name="strand" type="select" label="Query strand(s) to search against database/subject">
<option value="-strand both">Both</option>
<option value="-strand plus">Plus (forward)</option>
<option value="-strand minus">Minus (reverse complement)</option>
</param>
</when>
</conditional>
</inputs>