diff abims_xcms_fillPeaks.xml @ 30:6b5ed508f81f draft

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

--- a/abims_xcms_fillPeaks.xml	Tue Oct 24 11:48:31 2017 -0400
+++ b/abims_xcms_fillPeaks.xml	Tue Feb 13 04:44:47 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.0">
+<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.1.1">
 
     <description>Integrate a sample's signal in regions where peak groups are not represented to create new peaks in missing areas</description>
 
@@ -117,6 +117,7 @@
 Xcms.fillPeaks
 ==============
 
+-----------
 Description
 -----------
 
@@ -133,17 +134,18 @@
 
 
 
+-----------------
 Workflow position
 -----------------
 
 
 **Upstream tools**
 
-+------------------------+------------------+--------------------+------------+
-| Name                   | output file      | format             | parameter  |
-+========================+==================+====================+============+
-| xcms.group             | xset.group.RData | rdata.xcms.group   | RData file |
-+------------------------+------------------+--------------------+------------+
+========================= ================= ================== ==========
+Name                      output file       format             parameter
+========================= ================= ================== ==========
+xcms.group                xset.group.RData  rdata.xcms.group   RData file
+========================= ================= ================== ==========
 
 
 **Downstream tools**
@@ -156,11 +158,14 @@
 |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.
+
+
 **General schema of the metabolomic workflow**
 
 .. image:: xcms_fillpeaks_workflow.png
 
----------------------------------------------------
+
 
 -----------
 Input files
@@ -190,7 +195,26 @@
 
     | "MSW" is used for peaklists without retention-time information like those from direct-infusion spectra.
 
-@HELP_GET_PEAK_LIST@
+
+Get a Peak List
+---------------
+
+If 'true', the module generates two additional files corresponding to the peak list:
+- the variable metadata file (corresponding to information about extracted ions such as mass or retention time)
+- the data matrix (corresponding to related intensities)
+
+**decimal places for [mass or retention time] values in identifiers**
+
+    | Ions' identifiers are constructed as MxxxTyyy where 'xxx' is the ion median mass and 'yyy' the ion median retention time.
+    | Two parameters are used to adjust the number of decimal places wanted in identifiers for mass and retention time respectively.
+    | Theses parameters do not affect decimal places in columns other than the identifier one.
+
+**Reported intensity values**
+
+    | This parameter determines which values should be reported as intensities in the dataMatrix table; it correspond to xcms 'intval' parameter:
+    | - into: integrated area of original (raw) peak
+    | - maxo: maximum intensity of original (raw) peak
+    | - intb: baseline corrected integrated peak area (only available if peak detection was done by ‘findPeaks.centWave’)
 
 ------------
 Output files
@@ -200,7 +224,19 @@
 
     | Rdata file that will be used in the **CAMERA.annotate** or **xcms.summary** step of the workflow.
 
-@HELP_GET_PEAK_LIST_OUTPUTS@
+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.
 
 
 ---------------------------------------------------
@@ -217,7 +253,14 @@
 Parameters
 ----------
 
-    | **method**: chrom
+    | method -> **chrom**
+    | Get a Peak List -> **false**
+
+
+Output files
+------------
+
+    | **xset.fillPeaks.RData: RData file**
 
 
 ---------------------------------------------------
@@ -225,6 +268,10 @@
 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: change the management of the peaklist ids. The main ids remain the same as xcms generated. The export setiings now only add custom names in the variableMetadata tab (namecustom)