diff abims_xcms_group.xml @ 28:a18fc7554c6d draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298

--- a/abims_xcms_group.xml	Tue Oct 24 11:47:07 2017 -0400
+++ b/abims_xcms_group.xml	Tue Feb 13 04:43:21 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_group" name="xcms.group" version="2.1.0">
+<tool id="abims_xcms_group" name="xcms.group" version="2.1.1">
 
     <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>
 
@@ -15,6 +15,7 @@
         image '$image'
 
         xsetRdataOutput '$xsetRData'
+        rplotspdf '$rplotsPdf'
 
         method $methods.method
         #if $methods.method == "density":
@@ -97,7 +98,7 @@
 
     <outputs>
         <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
-        <data name="rplotsPdf" format="pdf" from_work_dir="Rplots.pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
+        <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
         <expand macro="output_peaklist" function="group"/>
         <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
     </outputs>
@@ -281,26 +282,29 @@
 Xcms.Group
 ==========
 
+-----------
 Description
 -----------
 
 After peak identification with xcmsSet, this tool groups the peaks which represent the same analyte across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time. Allows rejection of features, which are only partially detected within the replicates of a sample class.
 
 
+
+-----------------
 Workflow position
 -----------------
 
 **Upstream tools**
 
-+------------------------+-----------------+--------------------+------------+
-| Name                   | output file     | format             | parameter  |
-+========================+=================+====================+============+
-| xcms.xcmsSet           |  xset.RData     |  rdata.xcms.raw    | RData file |
-+------------------------+-----------------+--------------------+------------+
-| xcms.xcmsSet Merger    |  xset.RData     |  rdata.xcms.raw    | RData file |
-+------------------------+-----------------+--------------------+------------+
-| xcms.retcor            |  xset.RData     |  rdata.xcms.retcor | RData file |
-+------------------------+-----------------+--------------------+------------+
+========================= ================= =================== ==========
+Name                      output file       format              parameter
+========================= ================= =================== ==========
+xcms.xcmsSet              xset.RData        rdata.xcms.raw      RData file
+------------------------- ----------------- ------------------- ----------
+xcms.xcmsSet Merger       xset.RData        rdata.xcms.raw      RData file
+------------------------- ----------------- ------------------- ----------
+xcms.retcor               xset.RData        rdata.xcms.retcor   RData file
+========================= ================= =================== ==========
 
 
 **Downstream tools**
@@ -313,23 +317,23 @@
 |xcms.fillPeaks             | xset.RData      | rdata.xcms.group   |
 +---------------------------+--------------------------------------+
 
+The output file is an xcmsSet.RData file. You can continue your analysis using it in **xcms.retcor** tool as an next step and then **xcms.fillPeaks**.
+
 **General schema of the metabolomic workflow**
 
 .. image:: xcms_group_workflow.png
 
 
----------------------------------------------------
-
 -----------
 Input files
 -----------
 
 +---------------------------+-----------------------+
-| Parameter                 |   Format              |
+| Parameter : num + label   |   Format              |
 +===========================+=======================+
-| OR : RData file           |   rdata.xcms.raw      |
+| Or : RData file            |   rdata.xcms.raw     |
 +---------------------------+-----------------------+
-| OR : RData file           |   rdata.xcms.retcor   |
+| Or : RData file            |   rdata.xcms.retcor  |
 +---------------------------+-----------------------+
 
 
@@ -353,19 +357,22 @@
     | Groups peaks together across samples by creating a master peak list and assigning corresponding peaks from all samples. It is inspired by the alignment algorithm of mzMine.
 
 
-@HELP_GET_PEAK_LIST@
-
 ------------
 Output files
 ------------
 
+xset.group.Rplots.pdf
+
 xset.group.RData: rdata.xcms.group format
 
     | Rdata file that will be necessary in the third and fourth step of the workflow (xcms.retcor and xcms.fillpeaks).
 
-xset.group.Rplots.pdf
+
+------
 
-@HELP_GET_PEAK_LIST_OUTPUTS@
+.. class:: infomark
+
+The output file is an xset.group.RData file. You can continue your analysis using it in **xcms.retcor** tool.
 
 
 ---------------------------------------------------
@@ -383,12 +390,23 @@
 Parameters
 ----------
 
-    | **Method**: density
-    | **bw**: 10
-    | **minfrac**: 0.5
-    | **mzwid**: 0.05
-    | **Advanced options**: show
-    | **max**: 10
+    | Method -> **density**
+    | bw     -> **5**
+    | minfrac -> **0.3**
+    | mzwid    -> **0.01**
+    | Advanced options: **show**
+    | max -> **50**
+
+
+Output files
+------------
+
+    | **1) xset.RData: RData file**
+
+    | **2) Example of an xset.group.Rplots pdf file**
+
+.. image:: xcms_group.png
+        :width: 700
 
 
 ---------------------------------------------------
@@ -396,6 +414,10 @@
 Changelog/News
 --------------
 
+**Version 2.1.1 - 29/11/2017**
+
+- BUGFIX: To avoid issues with accented letter in the parentFile tag of the mzXML files, we changed a hidden mechanim to LC_ALL=C
+
 **Version 2.1.0 - 07/02/2017**
 
 - IMPROVEMENT: Add an option to export the peak list at this step without have to wait camara.annotate