diff abims_xcms_fillPeaks.xml @ 34:d8bac1291473 draft

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

--- a/abims_xcms_fillPeaks.xml	Thu Mar 08 05:55:04 2018 -0500
+++ b/abims_xcms_fillPeaks.xml	Tue Apr 03 11:40:32 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_fillpeaks.r
+        @COMMAND_RSCRIPT@/xcms_fillpeaks.r
 
         image '$image'
 
@@ -49,7 +50,7 @@
 
     <tests>
         <!--<test>
-            <param name="image" value="xset.group.retcor.group.RData"/>
+            <param name="image" value="xset.group.retcor.group.RData" ftype="rdata"/>
             <param name="method" value="chrom"/>
             <param name="zip_file" value="sacuri_dir_root.zip"  ftype="zip" />
             <assert_stdout>
@@ -63,7 +64,7 @@
         </test>-->
         <!-- Issue with fillpeaks because it seems that there are too many NA
         <test>
-            <param name="image" value="faahKO.xset.group.retcor.group.RData"/>
+            <param name="image" value="faahKO.xset.group.retcor.group.RData" ftype="rdata"/>
             <param name="method" value="chrom"/>
             <conditional name="peaklist">
                 <param name="peaklistBool" value="true" />
@@ -84,7 +85,7 @@
             <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
         </test>
         <test>
-            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData"/>
+            <param name="image" value="faahKO-single.xset.merged.group.retcor.group.RData" ftype="rdata"/>
             <param name="method" value="chrom"/>
             <conditional name="peaklist">
                 <param name="peaklistBool" value="true" />
@@ -105,7 +106,7 @@
             <output name="dataMatrix" file="faahKO.xset.group.retcor.group.fillPeaks.dataMatrix.tsv" />
         </test>-->
         <test>
-            <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData"/>
+            <param name="image" value="faahKO-single.xset.merged.group2.retcor2.group2.RData" ftype="rdata"/>
             <conditional name="peaklist">
                 <param name="peaklistBool" value="true" />
                 <param name="convertRTMinute" value="false" />
@@ -163,33 +164,20 @@
 
 **Downstream tools**
 
-+---------------------------+------------------+-----------------------+
-| Name                      | Output file      | Format                |
-+===========================+==================+=======================+
-|CAMERA.annotate            | xset.retcor.RData| rdata.xcms.fillpeaks  |
-+---------------------------+------------------+-----------------------+
-|xcms.summary               | xset.retcor.RData| rdata.xcms.fillpeaks  |
-+---------------------------+------------------+-----------------------+
-
-The output file **xset.fillpeaks** is a RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool as a following step of your workflow.
+=========================== ================== =======================
+Name                        Output file        Format
+=========================== ================== =======================
+CAMERA.annotate             xset.retcor.RData  rdata.xcms.fillpeaks
+--------------------------- ------------------ -----------------------
+xcms.summary                xset.retcor.RData  rdata.xcms.fillpeaks
+=========================== ================== =======================
 
 
 **General schema of the metabolomic workflow**
 
 .. image:: xcms_fillpeaks_workflow.png
 
-
-
------------
-Input files
------------
-
-+---------------------------+-----------------------+
-| Parameter : num + label   |   Format              |
-+===========================+=======================+
-| 1 : RData file            |   rdata.xcms.group    |
-+---------------------------+-----------------------+
-
+---------------------------------------------------
 
 ----------
 Parameters
@@ -211,43 +199,7 @@
 
     | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.
 
-xset.variableMetadata.tsv : tabular format
-
-    | Table containing information about ions; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
-
-xset.dataMatrix.tsv : tabular format
-
-    | Table containing ions' intensities; can be used as one input of **Quality_Metrics** or **Generic_filter** modules.
-
-------
-
-.. class:: infomark
-
-The output file is a xset.fillPeaks.RData file. You can continue your analysis using it in **CAMERA.annotate** or **xcms.summary** tool.
-
-
----------------------------------------------------
-
----------------
-Working example
----------------
-
-Input files
------------
-
-    | RData file -> **xset.retcor.RData**
-
-Parameters
-----------
-
-    | method -> **chrom**
-    | Get a Peak List -> **false**
-
-
-Output files
-------------
-
-    | **xset.fillPeaks.RData: RData file**
+@HELP_PEAKLIST_OUTPUT@
 
 
 ---------------------------------------------------