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Add -matrix option to BLASTP, BLASTX, TBLASTN and TBLASTX (doesn't apply to BLASTN)

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This commit is contained in:
Peter Cock
2010-10-05 16:48:50 +01:00
parent 3927b50873
commit 38b83c7d3e
4 changed files with 48 additions and 0 deletions
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tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+12
View File
@@ -11,6 +11,7 @@
-task $blast_type
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.matrix
-out $output1
-outfmt $out_format
-num_threads 8
@@ -56,10 +57,21 @@
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="matrix" 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="matrix" type="select" label="Scoring matrix">
<option value="-matrix BLOSUM62">BLOSUM62 (default)</option>
<option value="-matrix BLOSUM90">BLOSUM90</option>
<option value="-matrix BLOSUM80">BLOSUM80</option>
<option value="-matrix BLOSUM50">BLOSUM50</option>
<option value="-matrix BLOSUM45">BLOSUM45</option>
<option value="-matrix PAM250">PAM250</option>
<option value="-matrix PAM70">PAM70</option>
<option value="-matrix PAM30">PAM30</option>
</param>
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+12
View File
@@ -11,6 +11,7 @@
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.strand
$adv_opts.matrix
-out $output1
-outfmt $out_format
-num_threads 8
@@ -53,6 +54,7 @@
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="strand" type="hidden" value="" />
<param name="matrix" type="hidden" value="" />
</when>
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
@@ -62,6 +64,16 @@
<option value="-strand plus">Plus (forward)</option>
<option value="-strand minus">Minus (reverse complement)</option>
</param>
<param name="matrix" type="select" label="Scoring matrix">
<option value="-matrix BLOSUM62">BLOSUM62 (default)</option>
<option value="-matrix BLOSUM90">BLOSUM90</option>
<option value="-matrix BLOSUM80">BLOSUM80</option>
<option value="-matrix BLOSUM50">BLOSUM50</option>
<option value="-matrix BLOSUM45">BLOSUM45</option>
<option value="-matrix PAM250">PAM250</option>
<option value="-matrix PAM70">PAM70</option>
<option value="-matrix PAM30">PAM30</option>
</param>
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+12
View File
@@ -10,6 +10,7 @@
#end if
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.matrix
-out $output1
-outfmt $out_format
-num_threads 8
@@ -51,10 +52,21 @@
</param>
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="matrix" 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="matrix" type="select" label="Scoring matrix">
<option value="-matrix BLOSUM62">BLOSUM62 (default)</option>
<option value="-matrix BLOSUM90">BLOSUM90</option>
<option value="-matrix BLOSUM80">BLOSUM80</option>
<option value="-matrix BLOSUM50">BLOSUM50</option>
<option value="-matrix BLOSUM45">BLOSUM45</option>
<option value="-matrix PAM250">PAM250</option>
<option value="-matrix PAM70">PAM70</option>
<option value="-matrix PAM30">PAM30</option>
</param>
</when>
</conditional>
</inputs>
tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+12
View File
@@ -11,6 +11,7 @@
-evalue $evalue_cutoff
$adv_opts.filter_query
$adv_opts.strand
$adv_opts.matrix
-out $output1
-outfmt $out_format
-num_threads 8
@@ -53,6 +54,7 @@
<when value="basic">
<param name="filter_query" type="hidden" value="" />
<param name="strand" type="hidden" value="" />
<param name="matrix" type="hidden" value="" />
</when>
<when value="advanced">
<!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
@@ -62,6 +64,16 @@
<option value="-strand plus">Plus (forward)</option>
<option value="-strand minus">Minus (reverse complement)</option>
</param>
<param name="matrix" type="select" label="Scoring matrix">
<option value="-matrix BLOSUM62">BLOSUM62 (default)</option>
<option value="-matrix BLOSUM90">BLOSUM90</option>
<option value="-matrix BLOSUM80">BLOSUM80</option>
<option value="-matrix BLOSUM50">BLOSUM50</option>
<option value="-matrix BLOSUM45">BLOSUM45</option>
<option value="-matrix PAM250">PAM250</option>
<option value="-matrix PAM70">PAM70</option>
<option value="-matrix PAM30">PAM30</option>
</param>
</when>
</conditional>
</inputs>