diff delta_pi_calc.xml @ 1:8a30d6e5b97d draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3

--- a/delta_pi_calc.xml	Mon May 22 05:08:23 2017 -0400
+++ b/delta_pi_calc.xml	Mon Jul 24 05:25:22 2017 -0400
@@ -1,11 +1,25 @@
-<tool id="calc_delta_pi" name="Add delta pI" version="1.0">
+<tool id="calc_delta_pi" name="Add delta pI" version="1.1">
     <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'
+	    python '$__tool_directory__/peptide_pi_annotator.py' -i '$trainingpi' -p '$peptable' --out '$output'
+	    #if $stripcol
+	        --stripcol $stripcol
+	    #else if $stripcolpattern
+	        --stripcolpattern '$stripcolpattern'
+	    #end if
+	    #if $pepcol
+                --pepcol $pepcol 
+	    #else if $pepcolpattern
+                --pepcolpattern '$pepcolpattern'
+	    #end if
+	    #if $fraccol
+                --fraccol $fraccol
+	    #else if $fraccolpattern
+                --fraccolpattern '$fraccolpattern'
+	    #end if
 	    
 	    --strippatterns
 	    #for $strip in $strips
@@ -42,9 +56,12 @@
 	      </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"/>
+      <param name="pepcolpattern" type="text" value="" optional="true" label="Peptide sequence pattern for column header field in peptide table." />
+      <param name="pepcol" type="integer" value="" optional="true" label="Peptide sequence column number in peptide table. First column is 1. Overrides column pattern." />
+      <param name="fraccolpattern" type="text" value="" optional="true" label="Fraction number column header papttern in peptide table." />
+      <param name="fraccol" type="integer" optional="true" value="" label="Fraction number column number in peptide table. First column is 1. Overrides column pattern." />
+      <param name="stripcolpattern" type="text" optional="true" value="" label="Strip pattern header column pattern in peptide table" help="E.g. column with filename to derive strip name from"/>
+      <param name="stripcol" type="integer" optional="true" value="" label="Strip pattern column number in peptide table" help="E.g. column with filename to derive strip name from. First column is 1. Overrides column pattern"/>
       <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>
@@ -83,6 +100,27 @@
             </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="*" />
+            </repeat>
+            <param name="pepcolpattern" value="Sequence" />
+            <param name="fraccolpattern" value="Fraction" />
+            <param name="stripcolpattern" value="Filename" />
+            <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" />