xcms_fillpeaks: abims_xcms_fillPeaks.xml comparison

comparison abims_xcms_fillPeaks.xml @ 30:6b5ed508f81f draft

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

author	lecorguille
date	Tue, 13 Feb 2018 04:44:47 -0500
parents	f6d3e6be4ea3
children	8fd5b5afa24d

comparison

equal deleted inserted replaced

-:f6d3e6be4ea3
+:6b5ed508f81f
-<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>
 <macros>
 <import>macros.xml</import>
 ==============
 Xcms.fillPeaks
 ==============
+-----------
 Description
 -----------
 **Integrate areas of missing peaks**
 For each sample, identify peak groups where that sample is not
 "MSW" is used for peaklists without retention-time information
 like those from direct-infusion spectra.
+-----------------
 Workflow position
 -----------------
 **Upstream tools**
-+------------------------+------------------+--------------------+------------+
+========================= ================= ================== ==========
-| Name                   | output file      | format             | parameter  |
+Name                      output file       format             parameter
-+========================+==================+====================+============+
+========================= ================= ================== ==========
-| xcms.group             | xset.group.RData | rdata.xcms.group   | RData file |
+xcms.group                xset.group.RData  rdata.xcms.group   RData file
-+------------------------+------------------+--------------------+------------+
+========================= ================= ================== ==========
 **Downstream tools**
 +---------------------------+------------------+-----------------------+
 |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.
 **General schema of the metabolomic workflow**
 .. image:: xcms_fillpeaks_workflow.png
----------------------------------------------------
 -----------
 Input files
 -----------
 **MSW**
 | "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
 ------------
 xset.fillPeaks.RData : rdata.xcms.fillpeaks format
 | 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.
 ---------------------------------------------------
 ---------------
 | RData file -> **xset.retcor.RData**
 Parameters
 ----------
-| **method**: chrom
+| method -> **chrom**
+| Get a Peak List -> **false**
+Output files
+------------
+| **xset.fillPeaks.RData: RData file**
 ---------------------------------------------------
 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)
 - IMPROVEMENT: xcms.fillpeaks can deal with merged individual data

Mercurial > repos > lecorguille > xcms_fillpeaks

comparison abims_xcms_fillPeaks.xml @ 30:6b5ed508f81f draft