From b3bcbdcf153ebd5db0086cf38f21d3b3f8ac7fe8 Mon Sep 17 00:00:00 2001
From: Wen-Yu Chung <wychung@bx.psu.edu>
Date: Wed, 15 Oct 2008 15:51:13 -0400
Subject: [PATCH] update xml files for short reads mapping tools.

---
 tools/metag_tools/blat_wrapper.xml         |  2 +-
 tools/metag_tools/megablast_wrapper.xml    |  2 +-
 tools/metag_tools/shrimp_color_wrapper.xml |  8 ++++----
 tools/metag_tools/shrimp_wrapper.xml       | 13 +++++++------
 tools/sr_mapping/lastz_wrapper.xml         |  2 +-
 5 files changed, 14 insertions(+), 13 deletions(-)

diff --git a/tools/metag_tools/blat_wrapper.xml b/tools/metag_tools/blat_wrapper.xml
index 385f9e0d854..7d0451659c6 100644
--- a/tools/metag_tools/blat_wrapper.xml
+++ b/tools/metag_tools/blat_wrapper.xml
@@ -1,5 +1,5 @@
 <tool id="blat_wrapper" name="BLAT" version="1.0.0">
-  <description>: compare sequencing reads against UCSC genome builds</description>
+  <description> compare sequencing reads against UCSC genome builds</description>
   <command interpreter="python">
     #if $source.source_select=="database":#blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off
     #else:#blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off
diff --git a/tools/metag_tools/megablast_wrapper.xml b/tools/metag_tools/megablast_wrapper.xml
index 69b28a0dea4..9ed440632b8 100644
--- a/tools/metag_tools/megablast_wrapper.xml
+++ b/tools/metag_tools/megablast_wrapper.xml
@@ -1,5 +1,5 @@
 <tool id="megablast_wrapper" name="Megablast" version="1.0.0">
-	<description>: compare short reads against nt and wgs databases</description>
+	<description> compare short reads against nt and wgs databases</description>
 	<command interpreter="python">megablast_wrapper.py $source_select $input_query $output1 $word_size $iden_cutoff $evalue_cutoff $filter_query ${GALAXY_DATA_INDEX_DIR}</command>
 	<inputs>
 		<param name="source_select" type="select" display="radio" label="Choose target database">
diff --git a/tools/metag_tools/shrimp_color_wrapper.xml b/tools/metag_tools/shrimp_color_wrapper.xml
index 39307065e66..de2db722e48 100644
--- a/tools/metag_tools/shrimp_color_wrapper.xml
+++ b/tools/metag_tools/shrimp_color_wrapper.xml
@@ -1,5 +1,5 @@
-<tool id="shrimp_color_wrapper" name="SHRiMP : Color space" version="1.0.0">
-  <description> </description>
+<tool id="shrimp_color_wrapper" name="SHRiMP for Color-space" version="1.0.0">
+  <description>reads mapping against reference sequence </description>
   <command interpreter="python">
     #if     $param.skip_or_full=="skip":#shrimp_color_wrapper.py $input_target $input_query $output1 
     #else   #shrimp_color_wrapper.py $input_target $input_query $output1 $param.spaced_seed $param.seed_matches_per_window $param.seed_hit_taboo_length $param.seed_generation_taboo_length $param.seed_window_length $param.max_hits_per_read $param.max_read_length $param.kmer $param.sw_match_value $param.sw_mismatch_value $param.sw_gap_open_ref $param.sw_gap_open_query $param.sw_gap_ext_ref $param.sw_gap_ext_query $param.sw_crossover_penalty $param.sw_full_hit_threshold $param.sw_vector_hit_threshold  
@@ -7,7 +7,7 @@
   </command>
     <inputs>
         <page>
-        <param name="input_query" type="data" format="csfasta" label="Align sequencing reads" />
+        <param name="input_query" type="data" format="csfasta" label="Align sequencing reads" help="No dataset? Read tip below"/>
         <param name="input_target" type="data" format="fasta" label="against reference" />
         <conditional name="param">
             <param name="skip_or_full" type="select" label="SHRiMP settings to use" help="For most mapping needs use Commonly used settings. If you want full control use Full List">
@@ -55,7 +55,7 @@
     
 .. class:: warningmark 
 
-Please note that only **color-space** sequences can be used as query.   
+To use this tool your dataset needs to be in *csfasta* (as ABI SOLiD color-space sequences) format. Click pencil icon next to your dataset to set datatype to *csfasta*.   
 
 
 -----
diff --git a/tools/metag_tools/shrimp_wrapper.xml b/tools/metag_tools/shrimp_wrapper.xml
index bc5428acb7c..f1eb9cd6dd3 100644
--- a/tools/metag_tools/shrimp_wrapper.xml
+++ b/tools/metag_tools/shrimp_wrapper.xml
@@ -1,5 +1,5 @@
-<tool id="shrimp_wrapper" name="SHRiMP" version="1.0.0">
-  <description>: SHort Read Mapping Package</description>
+<tool id="shrimp_wrapper" name="SHRiMP for Letter-space" version="1.0.0">
+  <description>reads mapping against reference sequence </description>
   <command interpreter="python">
     #if     ($type_of_reads.single_or_paired=="single" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $input_target $output1 $output2 $input_query
     #elif   ($type_of_reads.single_or_paired=="paired" and $param.skip_or_full=="skip"):#shrimp_wrapper.py $input_target $output1 $output2 $type_of_reads.input1,$type_of_reads.input2,$type_of_reads.insertion_size
@@ -15,7 +15,7 @@
                 <option value="paired">Paired-end</option>
             </param>
             <when value="single">
-                <param name="input_query" type="data" format="fastqsolexa" label="Align sequencing reads" />
+                <param name="input_query" type="data" format="fastqsolexa" label="Align sequencing reads" help="No dataset? Read tip below"/>
             </when>
             <when value="paired">
                 <param name="insertion_size" type="integer" size="5" value="600" label="Insertion length between two ends" help="bp" />
@@ -124,10 +124,11 @@
         -->
     </tests>
 <help>
-    
-.. class:: warningmark 
 
-Please note that only **nucleotide** sequences (letter-space) can be used as query.   
+.. class:: warningmark
+
+IMPORTANT: This tool currently only supports data where the quality scores are integers or ASCII quality scores with base 64. Click pencil icon next to your dataset to set datatype to *fastqsolexa*.
+
 
 -----
     
diff --git a/tools/sr_mapping/lastz_wrapper.xml b/tools/sr_mapping/lastz_wrapper.xml
index 80c03460ea3..e3aabf57243 100644
--- a/tools/sr_mapping/lastz_wrapper.xml
+++ b/tools/sr_mapping/lastz_wrapper.xml
@@ -1,5 +1,5 @@
 <tool id="lastz_wrapper_1" name="Lastz" version="1.0.0">
-  <description>: map short reads against reference sequence</description>
+  <description> map short reads against reference sequence</description>
   <command>
     #if   ($params.source_select=="pre_set" and $seq_name.how_to_name=="No"  and $out_format.value=="diffs"):#lastz                     $input1 ${input2}[fullnames] --${params.pre_set_options} --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census=$output2 --coverage=$min_cvrg --format=$out_format  > $output1
     #elif ($params.source_select=="pre_set" and $seq_name.how_to_name=="Yes" and $out_format.value=="diffs"):#lastz $seq_name.ref_name::$input1 ${input2}[fullnames] --${params.pre_set_options} --ambiguousn --nolaj --identity=${min_ident}..${max_ident} --census=$output2 --coverage=$min_cvrg --format=$out_format  > $output1