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Make BLOSUM62 the default with sensible sorting (tip from Ross Lazarus on mailing list)

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Peter Cock
2010-10-05 16:52:33 +01:00
parent 38b83c7d3e
commit ef49c7ae2f
4 changed files with 5 additions and 4 deletions
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tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+1 -1
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@@ -63,9 +63,9 @@
<!-- 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 BLOSUM62" selected="true">BLOSUM62 (default)</option>
<option value="-matrix BLOSUM50">BLOSUM50</option>
<option value="-matrix BLOSUM45">BLOSUM45</option>
<option value="-matrix PAM250">PAM250</option>
tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+2 -1
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@@ -65,15 +65,16 @@
<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 BLOSUM62" selected="true">BLOSUM62 (default)</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
+1 -1
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@@ -58,9 +58,9 @@
<!-- 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 BLOSUM62" selected="true">BLOSUM62 (default)</option>
<option value="-matrix BLOSUM50">BLOSUM50</option>
<option value="-matrix BLOSUM45">BLOSUM45</option>
<option value="-matrix PAM250">PAM250</option>
tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+1 -1
View File
@@ -65,9 +65,9 @@
<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 BLOSUM62" selected="true">BLOSUM62 (default)</option>
<option value="-matrix BLOSUM50">BLOSUM50</option>
<option value="-matrix BLOSUM45">BLOSUM45</option>
<option value="-matrix PAM250">PAM250</option>