# HG changeset patch
# User bornea
# Date 1447179311 18000
# Node ID c88212194b4ec99deacd05129f3358e4af26145b
# Parent  6cafc67e8cda970c09f57d36fce92ef09a19d8c5
Uploaded

diff -r 6cafc67e8cda -r c88212194b4e SAINT_preprocessing_v5.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SAINT_preprocessing_v5.xml	Tue Nov 10 13:15:11 2015 -0500
@@ -0,0 +1,91 @@
+<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>
+  </requirments>
+  <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>