# HG changeset patch
# User lecorguille
# Date 1508860135 14400
# Node ID 33694028a409e393814009777269f27b843800f5
# Parent  e6a6503d7d6db2b39276a178d093c68ab35c9f75
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit bff1445c9b00ccdbe05ee3dc6ed24221033384b9

diff -r e6a6503d7d6d -r 33694028a409 abims_xcms_summary.xml
--- a/abims_xcms_summary.xml	Mon Apr 03 07:56:40 2017 -0400
+++ b/abims_xcms_summary.xml	Tue Oct 24 11:48:55 2017 -0400
@@ -51,31 +51,30 @@
 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
diff -r e6a6503d7d6d -r 33694028a409 macros.xml
--- a/macros.xml	Mon Apr 03 07:56:40 2017 -0400
+++ b/macros.xml	Tue Oct 24 11:48:55 2017 -0400
@@ -12,6 +12,7 @@
             <requirement type="package" version="1.46.0">bioconductor-xcms</requirement>
         </requirements>
     </xml>
+
     <xml name="stdio">
         <stdio>
             <exit_code range="1" level="fatal" />
@@ -116,14 +117,55 @@
         </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.
 
@@ -131,6 +173,57 @@
 
     </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>