# HG changeset patch
# User bornea
# Date 1447776236 18000
# Node ID a1bcd44fc605161a81ee0f6e6983466ede2894c7
# Parent  13383ba55336008a424a4abe38cda21d4ec2259e
Deleted selected files

diff -r 13383ba55336 -r a1bcd44fc605 SAINT_preprocessing_v5.xml
--- a/SAINT_preprocessing_v5.xml	Tue Nov 17 10:32:56 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-<tool id="SAINT_preprocessing_v5" name="SAINT pre-processing">
-  <description></description>
-  <command interpreter="python">
-    #if (str($type) == 'Scaffold'):
-      SAINT_preprocessing_v6.py $input $preybool $fasta_db $Inter_file $Prey_file 
-      "
-        #for $ba in $bait
-         ${ba.bait1}
-         ${ba.assign}
-         ${ba.T_C}
-        #end for
-        "
-      $Bait_file \$INSTALL_RUN_PATH/
-    #elif (str($type) == 'MaxQuant'):
-      SAINT_preprocessing_v6_mq_pep.py $input $preybool $fasta_db $Inter_file $Prey_file 
-        "
-        #for $ba in $bait
-          ${ba.bait1}
-          ${ba.assign}
-          ${ba.T_C}
-        #end for
-        "
-      $Bait_file \$INSTALL_RUN_PATH/
-    #end if
-  </command>
-  <requirements>
-    <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
-  </requirements>
-  <inputs>
-    <param type="select" name="type" label="MaxQuant or Scaffold">
-      <option value="MaxQuant">MaxQuant</option>
-      <option value="Scaffold">Scaffold</option> 
-    </param>
-    <param format="dat" name="input" type="data" label="Scaffold or MaxQuant proteinGroup Output"/>
-    <param type="boolean" name="preybool" checked="true" label="Create Prey File"/>
-    <param type="data" name="fasta_db" format="fasta"  label="Provide Uniprot Fasta database" />
-    <repeat name="bait" title="Bait Create">
-      <param name="bait1" type="text" size="100"/>
-      <param name="assign" type="text" size="100"/>
-      <param name="T_C" type="boolean" checked="true" label="Is this a Control?"/>
-    </repeat>
-  </inputs>
-  <outputs>
-    <data format="txt" name="Inter_file" label="Inter File"/>    
-    <data format="txt" name="Prey_file" label="Prey File" />
-    <data format="txt" name="Bait_file" label="Bait File" />
-  </outputs>
-  <stdio>
-    <regex match="error"
-	   source="stdout"
-           level="fatal"
-           description="Unknown error"/>
-    <regex match="Error: bad bait"
-           source="stdout"
-           level="fatal"
-           description="Error: bad bait"/>
-  </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>
-Pre-processing:
-APOSTL is able to recognize either a Scaffold "Samples Report" file (tab-delimited
-txt file) or the "peptides.txt" file output in the maxquant "txt" output folder. No
-modifications should be made to these files. Using the "Bait Create" tool, you can
-create your "bait.txt" file. It is important that the individual bait names match the
-bait names within your scaffold or maxquant output. APOSTL uses the bait file to find
-the user's baits of interest. Additionally there is an option to make the prey file (Y/N).
-When making a prey file, APOSTL queries uniprot in order to extract protein amino acid
-lengths and gene names. This takes several minutes depending on your internet connection. 
-Some users may want to run SAINTexpress using the same data set while changing which baits 
-are considered test or control. It is useful to toggle "Make Prey" off in order to save 
-time by circumventing this step as the same prey file can be used for both SAINTexpress 
-runs. 
-
-INPUTS:
-
-Scaffold file:
-
-- Scaffold "Samples Report" output (tab-delimited txt file)
-
-
-Maxquant file:
-
-- maxquant "peptides.txt" file (tab-delimited txt file)
-  </help>
-</tool>