From 38b83c7d3e4eed42a2e9f7ace533d80106ea2dc0 Mon Sep 17 00:00:00 2001
From: Peter Cock <p.j.a.cock@googlemail.com>
Date: Tue, 5 Oct 2010 16:48:50 +0100
Subject: [PATCH] Add -matrix option to BLASTP, BLASTX, TBLASTN and TBLASTX
 (doesn't apply to BLASTN)

---
 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml  | 12 ++++++++++++
 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml  | 12 ++++++++++++
 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml | 12 ++++++++++++
 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml | 12 ++++++++++++
 4 files changed, 48 insertions(+)

diff --git a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
index 6fe88f19000..308696eb02b 100644
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
@@ -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>
diff --git a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
index a90ddf1801c..47cccbb986d 100644
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
@@ -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>
diff --git a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
index b6f651dafb4..81a022add7a 100644
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
@@ -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>
diff --git a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
index 696eac45207..7fbef87ae72 100644
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
@@ -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>