--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/delta_pi_calc.xml	Mon May 22 05:08:23 2017 -0400
@@ -0,0 +1,146 @@
+<tool id="calc_delta_pi" name="Add delta pI" version="1.0">
+    <requirements>
+        <requirement type="package" version="3.6">python</requirement>
+    </requirements>
+    <description>to peptide table</description>
+    <command>
+	    python '$__tool_directory__/peptide_pi_annotator.py' -i '$trainingpi' -p '$peptable'
+            --stripcol $stripcol --pepcol $pepcol --fraccol $fraccol --out '$output'
+	    
+	    --strippatterns
+	    #for $strip in $strips
+	        '$strip.pattern'
+	    #end for
+
+	    --intercepts 
+	    #for $strip in $strips
+	        $strip.intercept 
+	    #end for
+	    
+	    --widths
+	    #for $strip in $strips
+		$strip.fr_width
+	    #end for
+	    
+	    #if len($ignoremods) > 0
+	        --ignoremods
+	        #for $mod in $ignoremods
+		    '$mod.regex'
+		#end for
+	    #end if
+    </command>
+    
+    <inputs>
+      <param name="trainingpi" type="data" format="tabular" label="Known peptides with annotation of pI" help="First column is sequence, second pI" />
+      <param name="peptable" type="data" format="tabular" label="Peptide table to determine pI shift from" />
+      <repeat name="ignoremods" title="Peptide modification weights to ignore">
+          <param name="regex" label="Regex to strip modification from peptide table before looking up sequence in predicted pI" type="text" help="Enter e.g. 15.994915 for oxidation, * to ignore all modifications, or a proper regex (however brackets are stripped by galaxy). See help below.">
+              <sanitizer>
+                  <valid>
+                      <remove preset="string.whitespace" /> 
+		  </valid>
+	      </sanitizer>
+          </param>
+      </repeat>
+      <param name="pepcol" type="integer" value="" label="Peptide sequence column in peptide table" />
+      <param name="fraccol" type="integer" value="" label="Fraction number column in peptide table" />
+      <param name="stripcol" type="integer" value="" label="Strip pattern column in peptide table" help="E.g. column with filename to derive strip name from"/>
+      <repeat name="strips" title="pI separation strip data">
+	      <param name="pattern" type="text" label="Strip regex detection pattern" help="Regex (see help below) that identifies the pI strip from the column in the above field.">
+                  <sanitizer>
+                      <valid>
+                          <remove preset="string.whitespace" />
+                      </valid>
+	          </sanitizer>
+              </param>
+	      <param name="intercept" type="text" label="pI intercept of strip" />
+	      <param name="fr_width" type="text" label="fraction widths" />
+     </repeat>
+    </inputs>
+    
+    <outputs>
+        <data format="tabular" name="output"/>
+    </outputs>
+    <tests>
+        <test> 
+            <param name="trainingpi" value="predicted_peptides.txt" />
+            <param name="peptable" value="peptable.txt" />
+            <repeat name="ignoremods">
+                <param name="regex" value="*" />
+            </repeat>
+            <param name="pepcol" value="1" />
+            <param name="fraccol" value="4" />
+            <param name="stripcol" value="2" />
+            <repeat name="strips">
+                <param name="pattern" value="strip1" />
+                <param name="intercept" value="8.21" />
+                <param name="fr_width" value="0.013" />
+            </repeat>
+            <repeat name="strips">
+                <param name="pattern" value="strip2" />
+                <param name="intercept" value="6.11" />
+                <param name="fr_width" value="0.04" />
+            </repeat>
+            <output name="output" value="peptable_deltapi.txt" />
+        </test>
+        <test>
+            <param name="trainingpi" value="predicted_peptides.txt" />
+            <param name="peptable" value="peptable.txt" />
+            <repeat name="ignoremods">
+                <param name="regex" value="15.994915" />
+            </repeat>
+            <param name="pepcol" value="1" />
+            <param name="fraccol" value="4" />
+            <param name="stripcol" value="2" />
+            <repeat name="strips">
+               <param name="pattern" value="strip1" />
+               <param name="intercept" value="8.21" />
+               <param name="fr_width" value="0.013" />
+            </repeat>
+            <repeat name="strips">
+               <param name="pattern" value="strip2" />
+               <param name="intercept" value="6.11" />
+               <param name="fr_width" value="0.04" />
+            </repeat>
+            <output name="output" value="peptable_deltapi.txt" />
+        </test>
+        <test>
+            <param name="trainingpi" value="predicted_peptides.txt" />
+            <param name="peptable" value="peptable.txt" />
+            <param name="pepcol" value="1" />
+            <param name="fraccol" value="4" />
+            <param name="stripcol" value="2" />
+            <repeat name="strips">
+                <param name="pattern" value="strip1" />
+                <param name="intercept" value="8.21" />
+                <param name="fr_width" value="0.013" />
+            </repeat>
+            <repeat name="strips">
+                <param name="pattern" value="strip2" />
+                <param name="intercept" value="6.11" />
+                <param name="fr_width" value="0.04" />
+            </repeat>
+            <output name="output" value="peptable_missed_ox.txt" />
+        </test>
+    </tests>
+
+    <help>
+	    In case you have no pI calculation method but a large table with 
+	    peptides and their predicted pIs available. This tool adds a column 
+	    with delta-pI values to a peptide or PSM table for each peptide it 
+	    can find in the predicted collection. Needs a tab-separated file 
+	    with peptide-sequences and their predicted pI, and a PSM/peptide table 
+	    with at least peptide sequences.
+
+	    Regexes, or regular expressions are are sequences of characters that 
+	    are used to find a certain pattern in a string of text. For example 
+	    the regex "peptide" will find the word "peptide" in the text
+	    "thisisa peptide in my sample". More advanced regexes can allow for
+	    finding for example specific but variable pieces of text, e.g.
+	    "[a-c].*" will match a string "acbcba" in "yxyzyxacbcbayxzyxyzxy".
+	    Much more elaborate regexes exist. Since this is a python script,
+	    python regexes are described here:
+	    https://docs.python.org/3/library/re.html
+    </help>
+
+</tool>