Mercurial > repos > galaxyp > hirieftools

diff pi_db_split.xml @ 1:8a30d6e5b97d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit ddcc42d2a767f7c14eb710b8ac264745c25444d3
author galaxyp
date Mon, 24 Jul 2017 05:25:22 -0400
parents 34c5c95740a1
children 77ddaee887a8
line wrap: on
line diff
--- a/pi_db_split.xml	Mon May 22 05:08:23 2017 -0400
+++ b/pi_db_split.xml	Mon Jul 24 05:25:22 2017 -0400
@@ -1,4 +1,4 @@
-<tool id="pi_db_split" name="Split peptide database" version="1.0">
+<tool id="pi_db_split" name="Split peptide database" version="1.1">
     <description>into pI separated fractions</description>
     <requirements>
         <requirement type="package">numpy</requirement>
@@ -8,14 +8,26 @@
 	    <![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 
+	    #for $strip in $strips
+	        #if not $strip.peptable_pattern or str($strip.peptable_pattern) in $peptable.element_identifier
+                    --intercept $strip.intercept --width $strip.fr_width --tolerance $strip.tolerance --amount $strip.fr_amount --prefix pisplit --picutoff $strip.picutoff 
+                    #if $strip.reverse
+                        --reverse
+                    #end if
+	            #break
+                #end if 
+            #end for
+
+	    #if $deltacol
+	        --deltacol $deltacol 
+            #else if $deltacolpattern
+		--deltacolpattern '$deltacolpattern'
+            #end if
 	    #if $fdrcol
 	        --fdrcol $fdrcol --fdrcutoff $fdrcutoff 
+            #else if $fdrcolpattern
+                --fdrcolpattern '$fdrcolpattern' --fdrcutoff $fdrcutoff 
 	    #end if
-            #if $reverse
-                --reverse
-            #end if
             #if $maxlen
                 --maxlen $maxlen
             #end if
@@ -26,17 +38,22 @@
     <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="fdrcolpattern" type="text" optional="true" label="FDR (q-value) column pattern in peptide table" />
+      <param name="fdrcol" type="integer" value="" optional="true" label="FDR (q-value) column number in peptide table" help="Overrides column pattern if filled. First column is 1" />
       <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="deltacolpattern" type="text" value="" label="Delta pI column pattern in peptide table" />
+      <param name="deltacol" type="integer" optional="true" value="" label="Delta pI column number in peptide table" help="Overrides column pattern if filled. First column is 1"/>
       <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)?" />
+      <repeat name="strips" title="pI separation strip data">
+          <param name="peptable_pattern" type="text" label="Pattern to find correct peptide table for a strip, for when multiple peptide tables have different strips" help="Will match against peptide table's name. Leave blank for single peptide table or when using same strip in all tables" />
+          <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)?" />
+          <param name="picutoff" type="float" value="0.2" optional="true" label="delta-pI cutoff for inclusion in shift determination" />
+      </repeat>
     </inputs>
     
     <outputs>
@@ -54,13 +71,42 @@
 		    <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" />
+                    <repeat name="strips">
+		        <param name="peptable_pattern" value="deltapi" />
+		        <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" />
+		        <param name="picutoff" value="10" />
+                    </repeat>
+		    <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>
+	    <test>
+		    <param name="pipeptides" value="predicted_peptides_to_split.txt" />
+		    <param name="peptable" value="peptable_deltapi.txt" />
+		    <param name="fdrcolpattern" value="FDR" />
+		    <param name="fdrcutoff" value="0.2" />
+		    <param name="deltacolpattern" value="Delta" />
+		    <param name="minlen" value="8" />
+                    <repeat name="strips">
+		        <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" />
+		        <param name="picutoff" value="10" />
+                    </repeat>
 		    <output_collection name="target_pi_db" type="list">
 			    <element name="fr1" value="target_splitdb_fr1.fasta" />
 			    <element name="fr2" value="target_splitdb_fr2.fasta" />