From 19592b4e39ba73bede215f77685f5aad2719ad28 Mon Sep 17 00:00:00 2001
From: Greg Von Kuster <greg@bx.psu.edu>
Date: Wed, 27 Jan 2010 08:51:23 -0500
Subject: [PATCH] Update tool_conf.xml.main and the tool conf for eupathdb.

---
 tool_conf.xml.main             | 24 +++++++++++++-----------
 tools/data_source/eupathdb.xml |  2 +-
 2 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/tool_conf.xml.main b/tool_conf.xml.main
index 28119c56039..b1fa2b78dc2 100644
--- a/tool_conf.xml.main
+++ b/tool_conf.xml.main
@@ -8,8 +8,6 @@
     <tool file="data_source/biomart.xml" />
     <tool file="data_source/gramene_mart.xml" />
     <tool file="data_source/flymine.xml" />
-    <tool file="data_source/modmine.xml" />
-    <tool file="data_source/ratmine.xml" />
     <tool file="data_source/eupathdb.xml" />
     <tool file="data_source/encode_db.xml" />
     <tool file="data_source/epigraph_import.xml" />
@@ -49,7 +47,6 @@
     <tool file="maf/maf_to_fasta.xml" />
     <tool file="fasta_tools/tabular_to_fasta.xml" />
     <tool file="fastx_toolkit/fastq_to_fasta.xml" />
-    <tool file="filters/wiggle_to_simple.xml" />
   </section>
   <section name="FASTA manipulation" id="fasta_manipulation">
     <tool file="fasta_tools/fasta_compute_length.xml" />
@@ -98,7 +95,7 @@
     <tool file="extract/phastOdds/phastOdds_tool.xml" />
   </section>
   <section name="Operate on Genomic Intervals" id="bxops">
-    <tool file="new_operations/intersect.xml" />  
+  	<tool file="new_operations/intersect.xml" />  
     <tool file="new_operations/subtract.xml" />
     <tool file="new_operations/merge.xml" />
     <tool file="new_operations/concat.xml" />
@@ -277,16 +274,20 @@
         <tool file="metag_tools/short_reads_figure_score.xml" />
         <tool file="metag_tools/short_reads_trim_seq.xml" />
     <label text="AB-SOLiD data" id="solid" />
-        <tool file="next_gen_conversion/solid_to_fastq.xml" />
+        <tool file="next_gen_conversion/solid2fastq.xml" />
         <tool file="solid_tools/solid_qual_stats.xml" />
         <tool file="solid_tools/solid_qual_boxplot.xml" />
   </section>
-  <section name="NGS: Mapping" id="solexa_tools">
-   <tool file="sr_mapping/bowtie_wrapper.xml" />
-   <tool file="sr_mapping/bwa_wrapper.xml" />
-  <!-- <tool file="sr_mapping/lastz_wrapper.xml" /> -->
-   <tool file="metag_tools/megablast_wrapper.xml" />
-   <tool file="metag_tools/megablast_xml_parser.xml" />
+  <section name="NGS: Mapping" id="ngs_mapping">
+    <label text="Illumina" />
+    <tool file="sr_mapping/bowtie_wrapper.xml" />
+    <tool file="sr_mapping/bwa_wrapper.xml" />
+    <label text="Roche-454" />
+    <tool file="sr_mapping/lastz_wrapper.xml" />
+    <tool file="metag_tools/megablast_wrapper.xml" />
+    <tool file="metag_tools/megablast_xml_parser.xml" />
+    <label text="AB-SOLiD" />
+    <tool file="sr_mapping/bowtie_color_wrapper.xml" />
   </section>
   <section name="NGS: SAM Tools" id="samtools">
    <tool file="samtools/sam_bitwise_flag_filter.xml" />
@@ -297,4 +298,5 @@
    <tool file="samtools/pileup_parser.xml" />
    <tool file="samtools/pileup_interval.xml" />
   </section>
+
 </toolbox>
diff --git a/tools/data_source/eupathdb.xml b/tools/data_source/eupathdb.xml
index 7d58a178eab..a004ab668b1 100644
--- a/tools/data_source/eupathdb.xml
+++ b/tools/data_source/eupathdb.xml
@@ -6,7 +6,7 @@
 <tool name="EuPathDB" id="eupathdb" tool_type="data_source">
     <description>server</description>
     <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
-    <inputs action="http://galaxy.eupathdb.org/eupathdb.galaxy/queries_tools.jsp" check_values="false" method="post"> 
+    <inputs action="http://eupathdb.org/eupathdb/queries_tools.jsp" check_values="false" method="post"> 
         <display>go to EuPathDB server $GALAXY_URL</display>
         <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" />
     </inputs>