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Don't default to setting seg/dust explicitly (allow BLAST+ to use its own defaults)

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This commit is contained in:
Peter Cock
2010-10-01 11:47:17 +01:00
parent a38f4f249b
commit 77fcdf4f4b
5 changed files with 20 additions and 15 deletions
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tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
+4 -3
View File
@@ -6,7 +6,7 @@
-db "$database"
-task $blast_type
-evalue $evalue_cutoff
-dust $adv_opts.filter_query
$adv_opts.filter_query
-out $output1
-outfmt $out_format
-num_threads 8
@@ -41,10 +41,11 @@
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="yes" />
<param name="filter_query" type="hidden" value="" />
</when>
<when value="advanced">
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="yes" falsevalue="no" checked="true" />
<!-- Could use a select (yes, no, other) where other allows setting 'level window linker' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with DUST)" truevalue="-dust yes" falsevalue="-dust no" checked="true" />
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+4 -3
View File
@@ -6,7 +6,7 @@
-db "$database"
-task $blast_type
-evalue $evalue_cutoff
-seg $adv_opts.filter_query
$adv_opts.filter_query
-out $output1
-outfmt $out_format
-num_threads 8
@@ -38,10 +38,11 @@
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="yes" />
<param name="filter_query" type="hidden" value="" />
</when>
<when value="advanced">
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" />
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+4 -3
View File
@@ -5,7 +5,7 @@
-query "$query"
-db "$database"
-evalue $evalue_cutoff
-seg $adv_opts.filter_query
$adv_opts.filter_query
-out $output1
-outfmt $out_format
-num_threads 8
@@ -33,10 +33,11 @@
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="yes" />
<param name="filter_query" type="hidden" value="" />
</when>
<when value="advanced">
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" />
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+4 -3
View File
@@ -5,7 +5,7 @@
-query "$query"
-db "$database"
-evalue $evalue_cutoff
-seg $adv_opts.filter_query
$adv_opts.filter_query
-out $output1
-outfmt $out_format
-num_threads 8
@@ -33,10 +33,11 @@
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="yes" />
<param name="filter_query" type="hidden" value="" />
</when>
<when value="advanced">
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" />
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+4 -3
View File
@@ -5,7 +5,7 @@
-query "$query"
-db "$database"
-evalue $evalue_cutoff
-seg $adv_opts.filter_query
$adv_opts.filter_query
-out $output1
-outfmt $out_format
-num_threads 8
@@ -33,10 +33,11 @@
<option value="advanced">Show Advanced Options</option>
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="yes" />
<param name="filter_query" type="hidden" value="" />
</when>
<when value="advanced">
<param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="yes" falsevalue="no" checked="true" />
<!-- 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" />
</when>
</conditional>
</inputs>