diff abims_CAMERA_combinexsAnnos.xml @ 8:198b035d4848 draft

planemo upload commit 301d42e88026afdac618f4ec56fc6cbe19e3e419

--- a/abims_CAMERA_combinexsAnnos.xml	Wed Feb 01 12:24:21 2017 -0500
+++ b/abims_CAMERA_combinexsAnnos.xml	Fri Apr 07 07:42:38 2017 -0400
@@ -1,7 +1,7 @@
-<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.4">
+<tool id="abims_CAMERA_combinexsAnnos" name="CAMERA.combinexsAnnos" version="2.0.6">
 
     <description>Wrapper function for the combinexsAnnos CAMERA function. Returns a dataframe with recalculated annotations.</description>
-    
+
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -11,20 +11,24 @@
 
     <command><![CDATA[
         @COMMAND_CAMERA_SCRIPT@
-        xfunction combinexsAnnos 
-        image_pos $image_pos 
-        image_neg $image_neg
+        xfunction combinexsAnnos
+        image_pos '$image_pos'
+        image_neg '$image_neg'
+
+        variableMetadataOutput '$variableMetadata'
 
-        variableMetadataOutput $variableMetadata
+        pos $pos tol $tol ruleset $ruleset keep_meta $keep_meta
 
-        pos $pos tol $tol ruleset $ruleset convert_param $convert_param keep_meta $keep_meta
-        
+        convertRTMinute $export.convertRTMinute
+        numDigitsMZ $export.numDigitsMZ
+        numDigitsRT $export.numDigitsRT
+
     ]]></command>
 
     <inputs>
         <param name="image_pos" type="data" label="Positive RData ion mode" format="rdata.camera.positive,rdata" help="output file from CAMERA.annotate using a positive polarity mode" />
         <param name="image_neg" type="data" label="Negative RData ion mode" format="rdata.camera.negative,rdata" help="output file from CAMERA.annotate using a positive negative mode" />
-    
+
         <param name="pos" type="select" label="Returned peaklist polarity mode">
             <option value="TRUE" selected="true">positive</option>
             <option value="FALSE" >negative</option>
@@ -32,9 +36,13 @@
 
         <param name="tol" type="integer" value="2" label="Retention time window in seconds" help="[pos] As first step it searches for pseudospectra from the positive and the negative sample within a retention time window" />
         <param name="ruleset" type="text" value="1,1" label="Matrix of matching rules" help="[ruleset] Matrix of matching rules. By default, the matrix (1,1) would create the M+H/M-H rule, since the first rule of xsa.pos@ruleset and xsa.neg@ruleset is M+H respectively M-H. Only rules with identical charge can be combined!" />
-        <param name="convert_param" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) rtmed, rtmin and rtmax into minutes"/>
         <param name="keep_meta" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE" label="Keep only the metabolites which match a difference "/>
 
+        <section name="export" title="Export options">
+            <param name="convertRTMinute" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Convert retention time (seconds) into minutes" help="Convert the columns rtmed, rtmin and rtmax into minutes"/>
+            <param name="numDigitsMZ" type="integer" value="4" label="Number of decimal places for mass values reported in ions' identifiers." help="A minimum of 4 decimal places is recommended. Useful to avoid duplicates within identifiers" />
+            <param name="numDigitsRT" type="integer" value="0" label="Number of decimal places for retention time values reported in ions' identifiers." help="Useful to avoid duplicates within identifiers" />
+        </section>
     </inputs>
 
     <outputs>
@@ -52,13 +60,18 @@
             <param name="pos" value="TRUE"/>
             <param name="tol" value="2"/>
             <param name="ruleset" value="1,1"/>
+            <section name="export">
+                <param name="convertRTMinute" value="True"/>
+                <param name="numDigitsMZ" value="4" />
+                <param name="numDigitsRT" value="1" />
+            </section>
             <output name="variableMetadata" file="faahOK.xset.group.retcor.group.fillPeaks.annotate.positive.combinexsAnnos.variableMetadata.tsv" />
         </test>
     </tests>
-    
-    
+
+
     <help><![CDATA[
-        
+
 @HELP_AUTHORS@
 
 =======================
@@ -100,11 +113,11 @@
 ========================= ======================= ===================== ==========
 Name                      Output file             Format                Parameter
 ========================= ======================= ===================== ==========
-xcms.annotatediffreport   xset.annotate_POS.RData rdata.camera.positive RData file        			
+xcms.annotatediffreport   xset.annotate_POS.RData rdata.camera.positive RData file
 ------------------------- ----------------------- --------------------- ----------
 xcms.annotatediffreport   xset.annotate_NEG.RData rdata.camera.positive RData file
 ========================= ======================= ===================== ==========
-  
+
 **Downstream tools**
 
 +---------------------------+-----------------------------------------+--------+
@@ -128,6 +141,10 @@
     | Multivariate PCA, PLS and OPLS
 
 
+**Place of CAMERA.combinexsannot after XCMS part of the metabolomic workflow**
+
+.. image:: combinexsannos_workflow_zoom.png
+
 **General schema of the metabolomic workflow**
 
 .. image:: combinexsannos_workflow.png
@@ -153,12 +170,12 @@
 
     | A tabular file which is similar to the diffreport result , within additional columns containing the annotation results.
     | For each metabolite (row) :
-    | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode 
+    | the value of the intensity in each sample, fold, tstat, pvalue, anova, mzmed, mzmin, mzmax, rtmed, rtmin, rtmax, npeaks, isotopes, adduct, pcgroup and neg (or pos). Mode
 
 xset.combinexsAnnos.Rdata
 
     | Rdata file, that be used outside Galaxy in R.
-    
+
 
 ---------------------------------------------------
 
@@ -192,6 +209,15 @@
 Changelog/News
 --------------
 
+**Version 2.0.6 - 10/02/2017**
+
+- IMPROVEMENT: Synchronize the variableMetadata export option with the other tools (xcms.group, xcms.fillpeaks, camera.annotate)
+
+
+**Version 2.0.5 - 22/12/2016**
+
+- IMPROVEMENT: add the possibility to add a personal Matrix of matching rules (ruleset)
+
 **Version 2.0.4 - 21/04/2016**
 
 - UPGRADE: upgrate the CAMERA version from 1.22.0 to 1.26.0
@@ -213,7 +239,7 @@
 
 **Version 2.0.0 - 09/06/2015**
 
-- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode 
+- NEW: combinexsAnnos Check CAMERA ion species annotation due to matching with opposite ion mode
 
 
     ]]></help>
@@ -222,5 +248,3 @@
 
 
 </tool>
- 
-