# HG changeset patch
# User bornea
# Date 1447175268 18000
# Node ID e911513d5ee3151cebf83861a99b60b89391c11a
# Parent  42883dfbb5d46393f8b87a00e95f1785fb964025
Deleted selected files

diff -r 42883dfbb5d4 -r e911513d5ee3 saint_wrapper.xml
--- a/saint_wrapper.xml	Tue Nov 10 12:02:55 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<tool id="saint_wrapper" name="SAINT">
-  <description></description>
-  <command interpreter="python">saint_wrapper.py $inter_input $prey_input $bait_input $rep_num $vc_bool $vc_num $go_bool $go_file $output</command>
-  <inputs>
-    <param format="txt" name="inter_input" type="data" label="Interactions File"/>
-    <param format="txt" name="prey_input" type="data" label="Prey File"/>
-    <param format="txt" name="bait_input" type="data" label="Bait File"/>
-    <param name="rep_num" type="integer" value="100" label="Number of Replicates" help="the number of replicates (with largest spectral counts or intensities) to be used for probability calculation in each bait.  This option is useful when some baits have more replicates than others." />
-    <param type="boolean" name="vc_bool" checked="false" label="Using Virtual Control Purifications by Compression"/>
-    <param name="vc_num" type="integer" value="1" label="Number of Virtual Controls" />
-    <param type="boolean" name="go_bool" checked="false" label="Incorporate External Data Sources" />
-    <param format="txt" name="go_file" type="data" optional="true" label="External Data File" help="SAINT can be run with the known interaction data in hand and it will incorporate the number of observed interactions into the statistics to boost identification probability."/>
-  </inputs>
-  <outputs>
-    <data format="txt" name="output" />
-  </outputs>
-  <stdio>
-    <regex match="error"
-	   source="stdout"
-           level="fatal"
-           description="Unknown error"/>
-  </stdio> 
-
-  <tests>
-    <test>
-      <param name="input" value="fa_gc_content_input.fa"/>
-      <output name="out_file1" file="fa_gc_content_output.txt"/>
-    </test>
-  </tests>
-  <help>
-  </help>
-</tool>
diff -r 42883dfbb5d4 -r e911513d5ee3 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Nov 10 12:02:55 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,19 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <!--<set_environment version="1.0">
-        <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR/bubblebeam</environment_variable>   
-    </set_environment>-->
-    <package name="saint_wrapper">
-        <install>
-            <actions>
-                <action type="shell_command">git clone http://github.com/bornea/Saint_On_Galaxy</action>
-                <action type="shell_command">unzip SAINTexpress_v3.6.1__2015-05-03.zip</action>
-                <action type="shell_command">./make -j</action>
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/Saint_On_Galaxy/SAINTexpress_v3.6.1__2015-05-03/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme></readme>
-    </package>
-</tool_dependency>
\ No newline at end of file