From 5f6112ecfa1824ab525e983c16e5261d4294153b Mon Sep 17 00:00:00 2001
From: Peter Cock <p.j.a.cock@googlemail.com>
Date: Wed, 13 Oct 2010 11:27:08 +0100
Subject: [PATCH] Workaround Issue 397 using 'if' in Cheetah template to avoid
 hidden parameters

---
 tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml  | 15 ++++++---------
 tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml  | 18 ++++++------------
 tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml  | 18 +++++++-----------
 tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml | 18 ++++++------------
 tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml | 17 +++++++----------
 5 files changed, 32 insertions(+), 54 deletions(-)

diff --git a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
index 6e71809176b..62a739b6307 100644
--- a/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml
@@ -12,11 +12,12 @@ blastn
 #end if
 -task $blast_type
 -evalue $evalue_cutoff
-$adv_opts.filter_query
-$adv_opts.strand
 -out $output1
 $out_format
 -num_threads 8
+#if $adv_opts.adv_opts_selector=="advanced":
+$adv_opts.filter_query
+$adv_opts.strand
 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -26,6 +27,8 @@ $out_format
 -word_size $adv_opts.word_size
 #end if
 $adv_opts.ungapped
+## End of advanced options:
+#end if
     </command>
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
@@ -78,13 +81,7 @@ $adv_opts.ungapped
               <option value="basic" selected="True">Hide Advanced Options</option>
               <option value="advanced">Show Advanced Options</option>
             </param>
-            <when value="basic">
-                <param name="filter_query" type="hidden" value="" />
-                <param name="strand" type="hidden" value="" />
-                <param name="max_hits" type="hidden" value="" />
-                <param name="word_size" type="hidden" value="" />
-                <param name="ungapped" type="hidden" value="" />
-            </when>
+            <when value="basic" />
             <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" />
diff --git a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
index 6861edb6edd..ad172a413e9 100644
--- a/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml
@@ -12,11 +12,12 @@ blastp
 #end if
 -task $blast_type
 -evalue $evalue_cutoff
-$adv_opts.filter_query
-$adv_opts.matrix
 -out $output1
 $out_format
 -num_threads 8
+#if $adv_opts.adv_opts_selector=="advanced":
+$adv_opts.filter_query
+$adv_opts.matrix
 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -27,6 +28,8 @@ $out_format
 #end if
 ##Ungapped disabled for now - see comments below
 ##$adv_opts.ungapped
+## End of advanced options:
+#end if
     </command>
     <inputs>
         <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
@@ -73,16 +76,7 @@ $out_format
               <option value="basic" selected="True">Hide Advanced Options</option>
               <option value="advanced">Show Advanced Options</option>
             </param>
-            <when value="basic">
-                <param name="filter_query" type="hidden" value="" />
-                <param name="matrix" type="hidden" value="" />
-                <param name="max_hits" type="hidden" value="" />
-                <param name="word_size" type="hidden" value="" />
-                <!--
-                Ungapped disabled for now, see comments below
-                <param name="ungapped" type="hidden" value="" />
-                -->
-            </when>
+            <when value="basic" />
             <when value="advanced">
                 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
                 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
diff --git a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
index 81bdaaf2970..5a176e62025 100644
--- a/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_blastx_wrapper.xml
@@ -11,12 +11,13 @@ blastx
   -subject "$db_opts.subject"
 #end if
 -evalue $evalue_cutoff
-$adv_opts.filter_query
-$adv_opts.strand
-$adv_opts.matrix
 -out $output1
 $out_format
 -num_threads 8
+#if $adv_opts.adv_opts_selector=="advanced":
+$adv_opts.filter_query
+$adv_opts.strand
+$adv_opts.matrix
 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -26,6 +27,8 @@ $out_format
 -word_size $adv_opts.word_size
 #end if
 $adv_opts.ungapped
+## End of advanced options:
+#end if
     </command>
     <inputs>
         <param name="query" type="data" format="fasta" label="Nucleotide query sequence(s)"/> 
@@ -68,14 +71,7 @@ $adv_opts.ungapped
               <option value="basic" selected="True">Hide Advanced Options</option>
               <option value="advanced">Show Advanced Options</option>
             </param>
-            <when value="basic">
-                <param name="filter_query" type="hidden" value="" />
-                <param name="strand" type="hidden" value="" />
-                <param name="matrix" type="hidden" value="" />
-                <param name="max_hits" type="hidden" value="" />
-                <param name="word_size" type="hidden" value="" />
-                <param name="ungapped" type="hidden" value="" />
-            </when>
+            <when value="basic" />
             <when value="advanced">
                 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
                 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
diff --git a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
index 1ddbd7c2d3f..6117b764d49 100644
--- a/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_tblastn_wrapper.xml
@@ -11,11 +11,12 @@ tblastn
   -subject "$db_opts.subject"
 #end if
 -evalue $evalue_cutoff
-$adv_opts.filter_query
-$adv_opts.matrix
 -out $output1
 $out_format
 -num_threads 8
+#if $adv_opts.adv_opts_selector=="advanced":
+$adv_opts.filter_query
+$adv_opts.matrix
 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -26,6 +27,8 @@ $out_format
 #end if
 ##Ungapped disabled for now - see comments below
 ##$adv_opts.ungapped
+## End of advanced options:
+#end if
     </command>
     <inputs>
         <param name="query" type="data" format="fasta" label="Protein query sequence(s)"/> 
@@ -68,16 +71,7 @@ $out_format
               <option value="basic" selected="True">Hide Advanced Options</option>
               <option value="advanced">Show Advanced Options</option>
             </param>
-            <when value="basic">
-                <param name="filter_query" type="hidden" value="" />
-                <param name="matrix" type="hidden" value="" />
-                <param name="max_hits" type="hidden" value="" />
-                <param name="word_size" type="hidden" value="" />
-                <!--
-                Ungapped disabled for now, see comments below
-                <param name="ungapped" type="hidden" value="" />
-                -->
-            </when>
+            <when value="basic" />
             <when value="advanced">
                 <!-- Could use a select (yes, no, other) where other allows setting 'window locut hicut' -->
                 <param name="filter_query" type="boolean" label="Filter out low complexity regions (with SEG)" truevalue="-seg yes" falsevalue="-seg no" checked="true" />
diff --git a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
index 66f2ff3a499..5e040a8413f 100644
--- a/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
+++ b/tools/ncbi_blast_plus/ncbi_tblastx_wrapper.xml
@@ -11,12 +11,13 @@ tblastx
   -subject "$db_opts.subject"
 #end if
 -evalue $evalue_cutoff
-$adv_opts.filter_query
-$adv_opts.strand
-$adv_opts.matrix
 -out $output1
 $out_format
 -num_threads 8
+#if $adv_opts.adv_opts_selector=="advanced":
+$adv_opts.filter_query
+$adv_opts.strand
+$adv_opts.matrix
 ## Need int(str(...)) because $adv_opts.max_hits is an InputValueWrapper object not a string
 ## Note -max_target_seqs overrides -num_descriptions and -num_alignments
 #if (str($adv_opts.max_hits) and int(str($adv_opts.max_hits)) > 0):
@@ -24,6 +25,8 @@ $out_format
 #end if
 #if (str($adv_opts.word_size) and int(str($adv_opts.word_size)) > 0):
 -word_size $adv_opts.word_size
+#end if
+## End of advanced options:
 #end if
     </command>
     <inputs>
@@ -67,13 +70,7 @@ $out_format
               <option value="basic" selected="True">Hide Advanced Options</option>
               <option value="advanced">Show Advanced Options</option>
             </param>
-            <when value="basic">
-                <param name="filter_query" type="hidden" value="" />
-                <param name="strand" type="hidden" value="" />
-                <param name="matrix" type="hidden" value="" />
-                <param name="max_hits" type="hidden" value="" />
-                <param name="word_size" type="hidden" value="" />
-            </when>
+            <when value="basic" />
             <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" />