# HG changeset patch
# User iracooke
# Date 1445906434 14400
# Node ID 1b86e378de378ef7419035b5b013b6cf251f48e4
# Parent  0746a2ae9e04cdd18627e56dc1bca708602ece01
Fix tabular outputs. Export XML_ONLY variable

diff -r 0746a2ae9e04 -r 1b86e378de37 interprophet.xml
--- a/interprophet.xml	Tue Oct 20 20:45:24 2015 -0400
+++ b/interprophet.xml	Mon Oct 26 20:40:34 2015 -0400
@@ -7,6 +7,8 @@
     </requirements>
     <command>
 <![CDATA[
+        export XML_ONLY="true";
+
         interprophet.rb --galaxy
         #if str( $input_type.type ) == "files":
             #for $pepxml_file in $input_type.pepxml_files:
diff -r 0746a2ae9e04 -r 1b86e378de37 peptide_prophet.xml
--- a/peptide_prophet.xml	Tue Oct 20 20:45:24 2015 -0400
+++ b/peptide_prophet.xml	Mon Oct 26 20:40:34 2015 -0400
@@ -6,6 +6,10 @@
         <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
     </requirements>
     <command>
+        # This should be in the tpp_package.
+        # A hack for now
+            export XML_ONLY="true";
+
         peptide_prophet.rb
             --galaxy $input_file
             -o peptide_prophet_output.pep.xml
diff -r 0746a2ae9e04 -r 1b86e378de37 pepxml_to_table.xml
--- a/pepxml_to_table.xml	Tue Oct 20 20:45:24 2015 -0400
+++ b/pepxml_to_table.xml	Mon Oct 26 20:40:34 2015 -0400
@@ -11,7 +11,7 @@
         <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
     </inputs>
     <outputs>
-        <data format="csv" name="output" metadata_source="input_file" label="${input_file.display_name}.csv" />
+        <data format="tabular" name="output" metadata_source="input_file" label="${input_file.display_name}.tsv" />
     </outputs>
     <tests>
         <!-- Just test that the tool runs and produces vaguely correct output -->
diff -r 0746a2ae9e04 -r 1b86e378de37 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Oct 20 20:45:24 2015 -0400
+++ b/tool_dependencies.xml	Mon Oct 26 20:40:34 2015 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="protk" version="1.4.3">
-        <repository changeset_revision="74bf855be117" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="991797b02976" name="package_protk_1_4_3" owner="iracooke" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="trans_proteomic_pipeline" version="4.8.0">
         <repository changeset_revision="a7273394d858" name="package_tpp_4_8_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />