diff abims_xcms_retcor.xml @ 34:9714270678a7 draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a

--- a/abims_xcms_retcor.xml	Thu Mar 08 05:54:22 2018 -0500
+++ b/abims_xcms_retcor.xml	Tue Apr 03 11:39:48 2018 -0400
@@ -4,13 +4,14 @@
 
     <macros>
         <import>macros.xml</import>
+        <import>macros_xcms.xml</import>
     </macros>
 
     <expand macro="requirements"/>
     <expand macro="stdio"/>
 
     <command><![CDATA[
-        @COMMAND_XCMS_SCRIPT@/xcms_retcor.r
+        @COMMAND_RSCRIPT@/xcms_retcor.r
         image '$image'
 
         method $methods.method
@@ -43,7 +44,7 @@
     ]]></command>
 
     <inputs>
-        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks" />
+        <param name="image" type="data" format="rdata.xcms.findchrompeaks,rdata.xcms.group,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks" />
         <conditional name="methods">
             <param name="method" type="select" label="Method to use for retention time correction" help="See the help section below" >
                 <option value="PeakGroups" selected="true">PeakGroups - retention time correction based on aligment of features (peak groups) present in most/all samples.</option>
@@ -132,7 +133,7 @@
 
     <tests>
         <test>
-            <param name="image" value="faahKO-single-class.xset.group.RData"/>
+            <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="PeakGroups"/>
                 <param name="extraPeaks" value="1"/>
@@ -160,7 +161,7 @@
         </test>
         <!-- DISABLE FOR TRAVIS : Zip
         <test>
-            <param name="image" value="faahKO.xset.group.RData"/>
+            <param name="image" value="faahKO.xset.group.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="PeakGroups"/>
                 <param name="extraPeaks" value="1"/>
@@ -187,7 +188,7 @@
         <!-- DISABLE FOR TRAVIS
         Test to test the different methods parameters
         <test>
-            <param name="image" value="faahKO-single-class.xset.group.RData"/>
+            <param name="image" value="faahKO-single-class.xset.group.RData" ftype="rdata"/>
             <conditional name="methods">
                 <param name="method" value="Obiwarp"/>
                 <section name="ObiwarpAdv">
@@ -245,39 +246,29 @@
 
 **Upstream tools**
 
-========================= ================= ======= ==========
-Name                      output file       format  parameter
-========================= ================= ======= ==========
-xcms.group                xset.group.RData  RData   RData file
-========================= ================= ======= ==========
+========================= ================= ============================== ==========
+Name                      output file       format                         parameter
+========================= ================= ============================== ==========
+xcms.xcmsSet              xset.RData        rdata.xcms.findchrompeaks      RData file
+------------------------- ----------------- ------------------------------ ----------
+xcms.group                xset.group.RData  RData                          RData file
+========================= ================= ============================== ==========
 
 
 **Downstream tools**
 
-+---------------------------+------------------+--------+
-| Name                      | Output file      | Format |
-+===========================+==================+========+
-|xcms.group                 | xset.retcor.RData| RData  |
-+---------------------------+------------------+--------+
-
-The output file **xset.retcor.RData** is an RData file. You can continue your analysis using it in **xcms.group** tool as an next step.
+=========================== ================== ========
+Name                        Output file        Format
+=========================== ================== ========
+xcms.group                  xset.retcor.RData  RData
+=========================== ================== ========
 
 
 **General schema of the metabolomic workflow**
 
 .. image:: xcms_retcor_workflow.png
 
-
------------
-Input files
------------
-
-+---------------------------+----------------------+
-| Parameter : num + label   |   Format             |
-+===========================+======================+
-| 1 : RData file            |   rdata.xcms.group   |
-+---------------------------+----------------------+
-
+---------------------------------------------------
 
 ----------
 Parameters
@@ -305,60 +296,11 @@
 Output files
 ------------
 
-xset.group.retcor.TICs_corrected.pdf
-
-    | "Total Ion Chromatograms" graph in pdf format,corrected after a retcor step.
-
-xset.group.retcor.BPCs_corrected.pdf
-
-    | "Total Io"Base Peak Chromatograms" graph in pdf format,corrected after a retcor step
-
 xset.group.retcor.RData: rdata.xcms.retcor format
 
     | Rdata file that will be necessary in the **xcms.group** step of the workflow.
 
 
-------
-
-.. class:: infomark
-
-The output file is an xset.retcor.RData file. You can continue your analysis using it in **xcms.fillPeaks** tool.
-
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
------------
-
-    | RData file -> **xset.group.RData**
-
-Parameters
-----------
-
-    | Method: -> **PeakGroups**
-    | smooth: -> **loess**
-    | extraPeaks: -> **1**
-    | minFraction -> **1**
-    | Advanced options: -> **show**
-    | span -> **0.2**
-    | family -> **gaussian**
-    | plottype -> **deviation**
-
-
-Output files
-------------
-
-    | **1) xset.group.retcor.RData: RData file**
-
-    | **2) Example of an xset.group.retcor.TICs_corrected pdf file**
-
-.. image:: xcms_retcor.png
-
-
 ---------------------------------------------------
 
 Changelog/News