--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pi_db_split.xml	Mon May 22 05:08:23 2017 -0400
@@ -0,0 +1,83 @@
+<tool id="pi_db_split" name="Split peptide database" version="1.0">
+    <description>into pI separated fractions</description>
+    <requirements>
+        <requirement type="package">numpy</requirement>
+        <requirement type="package" version="3.6">python</requirement>
+    </requirements>
+    <command>
+	    <![CDATA[
+	    mkdir pi_fr_out && cd pi_fr_out &&
+	    python '$__tool_directory__/pi_database_splitter.py' -i '$pipeptides' -p '$peptable'
+            --intercept $intercept --width $fr_width --tolerance $tolerance --amount $fr_amount --prefix pisplit
+	    --deltacol $deltacol --picutoff $picutoff 
+	    #if $fdrcol
+	        --fdrcol $fdrcol --fdrcutoff $fdrcutoff 
+	    #end if
+            #if $reverse
+                --reverse
+            #end if
+            #if $maxlen
+                --maxlen $maxlen
+            #end if
+            --minlen $minlen
+	    ]]>
+    </command>
+    
+    <inputs>
+      <param name="pipeptides" type="data" format="tabular" label="Target peptides with pI and accession" help="First col accession, second sequence, third pI" />
+      <param name="peptable" type="data" format="tabular" label="Peptide table to determine pI shift from" help="Should have delta pI as a column" />
+      <param name="fdrcol" type="integer" value="" optional="true" label="FDR (q-value) column in peptide table" />
+      <param name="fdrcutoff" type="float" value="0.0" help="Not used when no FDR column specified" label="FDR value cutoff for inclusion in shift determination" />
+      <param name="deltacol" type="integer" value="" label="Delta pI column in peptide table" />
+      <param name="picutoff" type="float" value="0.2" optional="true" label="delta-pI cutoff for inclusion in shift determination" />
+      <param name="minlen" type="integer" value="8" label="Minimum length of peptide to include in split DB" />
+      <param name="maxlen" type="integer" optional="true" value="" label="Max. length of peptide to include in split DB" />
+      <param name="intercept" type="float" value="" label="Intercept of pI strip" />
+      <param name="fr_width" type="float" value="" label="Fraction width" />
+      <param name="tolerance" type="float" value="" label="pI tolerance" />
+      <param name="fr_amount" type="integer" value="" label="Fraction amount" />
+      <param name="reverse" type="boolean" label="Strip is reversed (high-to-low pI)?" />
+    </inputs>
+    
+    <outputs>
+	<collection name="target_pi_db" type="list" label="target pI separated db">
+            <discover_datasets pattern="pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" />
+	</collection>
+	<collection name="decoy_pi_db" type="list" label="decoy pI separated db">
+            <discover_datasets pattern="decoy_pisplit_(?P&lt;designation&gt;.+)\.fasta" ext="fasta" directory="pi_fr_out" />
+	</collection>
+    </outputs>
+    <tests>
+	    <test>
+		    <param name="pipeptides" value="predicted_peptides_to_split.txt" />
+		    <param name="peptable" value="peptable_deltapi.txt" />
+		    <param name="fdrcol" value="3" />
+		    <param name="fdrcutoff" value="0.2" />
+		    <param name="deltacol" value="-1" />
+		    <param name="picutoff" value="10" />
+		    <param name="minlen" value="8" />
+		    <param name="intercept" value="5.6" />
+		    <param name="fr_width" value="1.3" />
+		    <param name="tolerance" value="0.1" />
+		    <param name="fr_amount" value="3" />
+		    <param name="reverse" value="false" />
+		    <output_collection name="target_pi_db" type="list">
+			    <element name="fr1" value="target_splitdb_fr1.fasta" />
+			    <element name="fr2" value="target_splitdb_fr2.fasta" />
+			    <element name="fr3" value="target_splitdb_fr3.fasta" />
+		    </output_collection>
+		    <output_collection name="decoy_pi_db" type="list">
+			    <element name="fr1" value="decoy_splitdb_fr1.fasta" />
+			    <element name="fr2" value="decoy_splitdb_fr2.fasta" />
+			    <element name="fr3" value="decoy_splitdb_fr3.fasta" />
+		    </output_collection>
+	    </test>
+    </tests>
+
+    <help>
+	    Creates a pI separated database collection from a pI-determined input
+	    file of peptide/protein mappings. Outputs one db for target, one
+	    for decoy.
+    </help>
+
+</tool>