diff abims_CAMERA_annotateDiffreport.xml @ 18:85b8351ded6c draft

planemo upload commit a57205d251bdebafdee164225fd03ac4d821e49c-dirty

--- a/abims_CAMERA_annotateDiffreport.xml	Mon Jul 04 11:57:04 2016 -0400
+++ b/abims_CAMERA_annotateDiffreport.xml	Wed Jul 06 17:28:55 2016 -0400
@@ -1,4 +1,4 @@
-<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.5">
+<tool id="abims_CAMERA_annotateDiffreport" name="CAMERA.annotate" version="2.1.6">
 
     <description>CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.</description>
     
@@ -33,7 +33,11 @@
             calcCiS $quick_block.calcCiS
             calcIso $quick_block.calcIso
             calcCaS $quick_block.calcCaS
-            multiplier $quick_block.multiplier
+            #if $quick_block.rules_block.rules_select == "FALSE"
+                multiplier $quick_block.rules_block.multiplier
+            #else
+                multiplier $quick_block.rules_block.rules
+            #end if
         #end if
 
         #if $options.option == "show":
@@ -94,14 +98,24 @@
                 <param name="calcCiS" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation inside samples for peak grouping" help="[calcCiS]"/>
                 <param name="calcIso" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use isotopic relationship for peak grouping" help="[calcIso]"/>
                 <param name="calcCaS" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="groupCorr: Use correlation across samples for peak grouping" help="[calcCaS]"/>
-                <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" />
+                <conditional name="rules_block">
+                    <param name="rules_select" type="select" label="Use a personal ruleset file">  
+                        <option value="TRUE">TRUE</option>
+                        <option value="FALSE" selected="true">FALSE</option>
+                    </param>
+                    <when value="FALSE">
+                        <param name="multiplier" type="integer" value="3" label="findAdducts: If no ruleset is provided, calculate ruleset with max. number n of [nM+x] clusterions" help="[multiplier]" /> 
+                    </when>
+                    <when value="TRUE">
+                        <param name="rules" type="data" format="csv" label="findAdducts: User defined ruleset" help="[rules]" />
+                    </when>
+                </conditional>
             </when>	
-                <when value="TRUE">
+            <when value="TRUE">
                 <param name="polarity" type="hidden" value="quick" label="for the output label" help="for the output label" />
             </when>	
         </conditional>
-                           
-    
+
         <!-- Annotatediffreport specific parameters -->
         <conditional name="options">
             <param name="option" type="select" label="Number of condition">
@@ -396,6 +410,10 @@
 Changelog/News
 --------------
 
+**Version 2.1.6 - 06/07/2016**
+
+- IMPROVEMENT: add the possibility to use defined ruleset
+
 **Version 2.1.5 - 21/04/2016**
 
 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0