# HG changeset patch
# User lecorguille
# Date 1518515113 18000
# Node ID 8ad83969888bdfc70a816c6f3e52e85fc3d03a7f
# Parent  33694028a409e393814009777269f27b843800f5
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 73791d74546087b2a872d9279df960f5bc207298

diff -r 33694028a409 -r 8ad83969888b README.rst
--- a/README.rst	Tue Oct 24 11:48:55 2017 -0400
+++ b/README.rst	Tue Feb 13 04:45:13 2018 -0500
@@ -2,6 +2,10 @@
 Changelog/News
 --------------
 
+**Version 1.0.4 - 13/02/2018**
+
+- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
+
 **Version 1.0.3 - 03/02/2017**
 
 - IMPROVEMENT: xcms.summary can deal with merged individual data
diff -r 33694028a409 -r 8ad83969888b abims_xcms_summary.xml
--- a/abims_xcms_summary.xml	Tue Oct 24 11:48:55 2017 -0400
+++ b/abims_xcms_summary.xml	Tue Feb 13 04:45:13 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.3">
+<tool id="abims_xcms_summary" name="xcms.summary" version="1.0.4">
 
     <description>Create a summary of XCMS analysis</description>
 
@@ -7,7 +7,7 @@
     </macros>
 
     <requirements>
-        <requirement type="package" version="1.26.0">bioconductor-camera</requirement>
+        <requirement type="package" version="1.32.0">bioconductor-camera</requirement>
         <requirement type="package" version="1.1_4">r-batch</requirement>
     </requirements>
 
@@ -51,30 +51,31 @@
 Xcms.summary
 ============
 
+-----------
 Description
 -----------
 
 This tool provide a HTML summary which summarizes your analysis using the [W4M] XCMS and CAMERA tools
 
-
+-----------------
 Workflow position
 -----------------
 
 **Upstream tools**
 
-+------------------------+------------------+----------------------+------------+
-| Name                   | output file      | format               | parameter  |
-+========================+==================+======================+============+
-| xcms.xcmsSet           | xset.RData       | rdata.xcms.raw       | RData file |
-+------------------------+------------------+----------------------+------------+
-| xcms.group             | xset.RData       | rdata.xcms.group     | RData file |
-+------------------------+------------------+----------------------+------------+
-| xcms.retcor            | xset.RData       | rdata.xcms.retcor    | RData file |
-+------------------------+------------------+----------------------+------------+
-| xcms.fillpeaks         | xset.RData       | rdata.xcms.fillpeaks | RData file |
-+------------------------+------------------+----------------------+------------+
-| CAMERA.annotate        | xset.RData       | rdata.camera.*       | RData file |
-+------------------------+------------------+----------------------+------------+
+========================= ================= ===================== ==========
+Name                      output file       format                parameter
+========================= ================= ===================== ==========
+xcms.xcmsSet              xset.RData        rdata.xcms.raw        RData file
+------------------------- ----------------- --------------------- ----------
+xcms.group                xset.RData        rdata.xcms.group      RData file
+------------------------- ----------------- --------------------- ----------
+xcms.retcor               xset.RData        rdata.xcms.retcor     RData file
+------------------------- ----------------- --------------------- ----------
+xcms.fillpeaks            xset.RData        rdata.xcms.fillpeaks  RData file
+------------------------- ----------------- --------------------- ----------
+CAMERA.annotate           xset.RData        rdata.camera.*        RData file
+========================= ================= ===================== ==========
 
 
 .. image:: xcms_summary_workflow.png
@@ -84,6 +85,10 @@
 Changelog/News
 --------------
 
+**Version 1.0.4 - 13/02/2018**
+
+- UPGRADE: upgrate the CAMERA version from 1.26.0 to 1.32.0
+
 **Version 1.0.3 - 03/02/2017**
 
 - IMPROVEMENT: xcms.summary can deal with merged individual data
diff -r 33694028a409 -r 8ad83969888b macros.xml
--- a/macros.xml	Tue Oct 24 11:48:55 2017 -0400
+++ b/macros.xml	Tue Feb 13 04:45:13 2018 -0500
@@ -12,7 +12,6 @@
             <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
         </requirements>
     </xml>
-
     <xml name="stdio">
         <stdio>
             <exit_code range="1" level="fatal" />
@@ -20,7 +19,7 @@
     </xml>
 
     <token name="@COMMAND_XCMS_SCRIPT@">
-        LANG=C Rscript $__tool_directory__/xcms.r
+        LC_ALL=C Rscript $__tool_directory__/xcms.r
     </token>
 
     <token name="@COMMAND_LOG_EXIT@">
@@ -117,55 +116,14 @@
         </data>
     </xml>
 
-    <xml name="input_tic_bpc_pdf">
-        <param name="tic_bpc_pdf" type="boolean" checked="False" label="Do you want TIC and BCP in PDF Format" help="Whatever, you will be able to use MultiQC tools on the tabular files" />
-    </xml>
-
-    <xml name="test_retcor_param">
-        <param name="methods|method" value="peakgroups"/>
-        <param name="methods|smooth" value="loess"/>
-        <param name="methods|extra" value="1"/>
-        <param name="methods|missing" value="1"/>
-        <param name="methods|options|option" value="show"/>
-        <param name="methods|options|span" value="0.2"/>
-        <param name="methods|options|family" value="gaussian"/>
-        <param name="methods|options|plottype" value="deviation"/>
-    </xml>
-
-    <xml name="test_retcor_output" token_raworcorrected="">
-        <output name="log">
-            <assert_contents>
-                <has_text text="object with 4 samples" />
-                <has_text text="Time range: 2507.7-4481.7 seconds (41.8-74.7 minutes)" />
-                <has_text text="Mass range: 200.1-600 m/z" />
-                <has_text text="Peaks: 9251 (about 2313 per sample)" />
-                <has_text text="Peak Groups: 0" />
-                <has_text text="Sample classes: KO, WT" />
-            </assert_contents>
-        </output>
-        <output_collection name="ticsCorrectedTabCollection" type="list">
-            <element name="ko15" value="ko15-TIC@RAWORCORRECTED@_mqc.out" />
-            <element name="ko16" value="ko16-TIC@RAWORCORRECTED@_mqc.out" />
-            <element name="wt15" value="wt15-TIC@RAWORCORRECTED@_mqc.out" />
-            <element name="wt16" value="wt16-TIC@RAWORCORRECTED@_mqc.out" />
-        </output_collection>
-        <output_collection name="bpcsCorrectedTabCollection" type="list">
-            <element name="ko15" value="ko15-BPC@RAWORCORRECTED@_mqc.out" />
-            <element name="ko16" value="ko16-BPC@RAWORCORRECTED@_mqc.out" />
-            <element name="wt15" value="wt15-BPC@RAWORCORRECTED@_mqc.out" />
-            <element name="wt16" value="wt16-BPC@RAWORCORRECTED@_mqc.out" />
-        </output_collection>
-    </xml>
-
     <token name="@HELP_AUTHORS@">
-
 .. class:: infomark
 
 **Authors**  Colin A. Smith csmith@scripps.edu, Ralf Tautenhahn rtautenh@gmail.com, Steffen Neumann sneumann@ipb-halle.de, Paul Benton hpaul.benton08@imperial.ac.uk and Christopher Conley cjconley@ucdavis.edu
 
 .. class:: infomark
 
-**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station Biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
+**Galaxy integration** ABiMS TEAM - UPMC/CNRS - Station biologique de Roscoff and Yann Guitton yann.guitton@oniris-nantes.fr - part of Workflow4Metabolomics.org [W4M]
 
  | Contact support@workflow4metabolomics.org for any questions or concerns about the Galaxy implementation of this tool.
 
@@ -173,57 +131,6 @@
 
     </token>
 
-    <token name="@HELP_BCP_TIC@">
-
-BPCs and TICs: tabular
-
-    | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs
-    | Import BPC and TIC from xcmsSet and retcor [at once] within MultiQC_ (in or outside Galaxy) to display and navigate in the graphs.
-    | - In MultiQC: as tool, use the Custom Content
-
-.. _MultiQC: http://multiqc.info/
-
-BPCs and TICs: pdf [if using zip]
-
-    | "Base Peak Chromatograms" and "Total Ion Chromatograms" graphs in pdf format.
-
-    </token>
-
-    <token name="@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’)
-
-    </token>
-
-    <token name="@HELP_GET_PEAK_LIST_OUTPUTS@">
-
-xset.variableMetadata.tsv : tabular format [If Get a Peak List == Yes]
-
-    | Table containing information about ions - Can be used in **Normalisation/Generic_filter** and **Statitics** tools.
-
-xset.dataMatrix.tsv : tabular format
-
-    | Table containing ions' intensities - Can be used **Normalisation/Generic_filter** and **Statitics** tools.
-
-    </token>
 
     <xml name="citation">
         <citations>