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+++ b/metaMS_plot.xml	Wed Jul 03 05:08:14 2019 -0400
@@ -0,0 +1,266 @@
+ <tool id="metams_plot" name="metaMS.plot" version="1.0.0">
+
+    <description>GC-MS data preprocessing using metaMS package</description>
+
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    
+    <expand macro="requirements">
+        <requirement type="package" version="9.22">ghostscript</requirement>
+    </expand>
+    <expand macro="stdio"/>
+
+    <command><![CDATA[
+    @COMMAND_RSCRIPT@/metaMS_plot.r
+        
+        metaMS '$metaMS'
+
+        selecttic $selectedtic
+
+        selectbpc $selectedbpc
+
+        selecteic $selectedeic.EIC
+        
+        #if $selectedeic.EIC == "true"
+            unkn "c($selectedeic.unkn)"
+        #else
+            unkn "none"
+        #end if
+
+        @COMMAND_FILE_LOAD@
+
+    ]]></command>
+
+    <inputs>
+
+        <param name="metaMS" type="data" format="rdata" label="Rdata from new_metaMS_runGC" help="Rdata file containing a metaMS preprocess object" />
+        <param name="selectedtic" type="boolean" checked="false" falsevalue="false" truevalue="true" label="Do you want to process for TIC(s) ?" />
+        <param name="selectedbpc" checked="false" falsevalue="false" truevalue="true" label="Do you want to process for BPC(s) ?"  type="boolean" />
+
+        <conditional name="selectedeic">
+            <param name="EIC" checked="false" falsevalue="false" truevalue="true" label="Do you want to process for EIC(s) ?"  type="boolean">
+                <option value="false">no</option>
+                <option value="true">yes</option>
+            </param>
+            <when value="true">
+                <param name="unkn" type="text" value="1:5" label="EIC_Unknown" help="vector of peaks number to be plotted, for example 1:5 (mean 1 to 5) or 1,4,12  (means 1 4 and 12). For all EIC use 0" /> 
+            </when>
+            <when value="false"/>
+        </conditional>
+
+        <expand macro="input_file_load"/>
+
+    </inputs>
+
+    <outputs>
+    
+        <!-- Only when user selected TIC option -->
+        <data name="ticsRawPdf"   format="pdf" from_work_dir="TICs_raw.pdf" label="TICs_raw.pdf">
+            <filter>selectedtic is True</filter>
+        </data>
+        <!-- Only when user selected BPC option -->
+        <data name="bpcsRawPdf"   format="pdf" from_work_dir="BPCs_raw.pdf" label="BPCs_raw.pdf">
+            <filter>selectedbpc is True</filter>
+        </data>
+        <!-- Only when user selected EIC option -->
+        <data name="unknownPdf"   format="pdf" from_work_dir="GCMS_EIC.pdf" label="GCMS_EIC.pdf">
+            <filter>selectedeic['EIC'] is True</filter>
+        </data>
+
+    </outputs>
+
+    <tests>
+
+        <!-- Test TIC -->
+        <test>
+            <param name="metaMS" value="runGC_test.RData"  ftype="rdata" />
+            <expand macro="test_file_load_alg_symlink" />
+            <param name="selectedtic" value="true"/>
+            <output name="ticsRawPdf" value="TICs_raw.pdf" ftype="pdf" compare="sim_size" delta="600"/>
+        </test>
+        <!-- Test BPC -->
+        <test>
+            <param name="metaMS" value="runGC_noDB.RData"  ftype="rdata" />
+            <expand macro="test_file_load_alg_symlink" />
+            <param name="selectedbpc" value="true"/>
+            <output name="bpcsRawPdf" value="BPCs_raw.pdf" ftype="pdf" compare="sim_size" delta="2000"/>
+        </test>
+        <!-- Test EICs -->
+        <test>
+            <param name="metaMS" value="runGC_noDB.RData"  ftype="rdata" />
+            <expand macro="test_file_load_alg_symlink" />
+            <conditional name="selectedeic">
+                <param name="EIC" value="true"/>
+                <param name="unkn" value="1:5"/>
+            </conditional>
+            <output name="unknownPdf" value="GCMS_EIC_noDB.pdf" ftype="pdf" compare="sim_size" delta="1200"/>
+        </test>
+
+        <!-- Tests with DB comparison -->
+        <!-- Test TIC -->
+        <!--<test>
+            <param name="metaMS" value="runGC.RData"  ftype="rdata" />
+            <param name="selectedtic|TIC" value="true"/>
+            <output name="ticsRawPdf" value="TICs_raw.pdf" ftype="pdf" compare="sim_size" delta="600"/>
+        </test>
+        --><!-- Test BPC -->
+        <!--<test>
+            <param name="metaMS" value="runGC.RData"  ftype="rdata" />
+            <param name="selectedbpc|BPC" value="true"/>
+            <output name="bpcsRawPdf" value="BPCs_raw.pdf" ftype="pdf" compare="sim_size" delta="600"/>
+        </test>
+        --><!-- Test EICs -->
+        <!--<test>
+            <param name="metaMS" value="runGC.RData"  ftype="rdata" />
+            <param name="selectedeic|EIC" value="true"/>
+            <output name="unknownPdf" value="GCMS_EIC.pdf" ftype="pdf" compare="sim_size" delta="600"/>
+        </test>
+-->
+    </tests>
+    
+    <help>
+
+<!--
+TODO : Add test on EICs (problem with gs not found whereas I added pip install ghostscript and bgs in .travis.yml)
+-->
+
+.. class:: infomark
+
+**Author(s)**  Ron Wehrens (ron.wehrens@gmail.com), Georg Weingart, Fulvio Mattivi
+
+.. class:: infomark
+
+**Galaxy wrapper and scripts developpers** Guitton Yann LABERCA yann.guitton@oniris-nantes.fr and Saint-Vanne Julien julien.saint-vanne@sb-roscoff.fr
+
+.. class:: infomark
+
+**Please cites**  
+ 
+ metaMS : Wehrens, R.; Weingart, G.; Mattivi, F. Journal of Chromatography B.
+
+ xcms :   Smith, C. A.; Want, E. J.; O’Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779–787.
+
+
+---------------------------------------------------
+
+====================
+metaMS_plot
+====================
+------------
+Description
+------------
+
+This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments.
+
+It will compare with opposite graphs your different classes given by a samplemetadata file or from xcms.findchrompeaks Merger tool.
+
+It can also make EICs from your unknowns that you choose, with their pseudospectra.
+  
+
+-----------------
+Workflow position
+-----------------
+
+
+**Upstream tools**
+
+You must use result file from :
+
+========================= ==================== ======= ==========
+Name                      output file          format  parameter
+========================= ==================== ======= ==========
+metaMS_runGC              runGC.RData           RData   file                     
+========================= ==================== ======= ==========
+
+
+
+**General schema of the metabolomic workflow for GCMS**
+
+.. image:: workflow_metaMS_plot.png
+
+-----------
+Input files
+-----------
+
+This tool always take files output from metaMS_runGC
+
++---------------------------+------------+
+| Parameter : num + label   |   Format   |
++===========================+============+
+| 1 : RData file            |   RData    |
++---------------------------+------------+
+
+
+----------
+Parameters
+----------
+
+There is no specific parameters except the choice for your EICs.
+
+----------
+Outputs
+----------
+
+According to your choice(s), you can have different output(s) :
+
+- The output file **BPCs_raw.pdf** is a pdf file where each page contain BPC of a class opposed to an other class.
+- The output file **TICs_raw.pdf** is a pdf file where each page contain TIC of a class opposed to an other class.
+- The output file **GCMS_EIC.pdf** is a pdf file where pages contain EICs from each sample for each unknown of your choice.
+
+
+----------------
+Working Example
+----------------
+.. class:: warningmark  
+
+**Reference Data for testing are taken from:**
+
+Dittami,S.M. et al. (2012) *Towards deciphering dynamic changes and evolutionary mechanisms involved in the adaptation to low salinities in Ectocarpus (brown algae): Adaptation to low salinities in Ectocarpus.* The Plant Journal
+
+Input files
+-----------
+
+    | **RData file** -> runGC_test.RData
+
+Parameters
+----------
+
+    | TIC -> **TRUE**
+    | BPC -> **TRUE**
+    | EIC -> **TRUE**
+        | Unkn -> **1-5**
+
+
+Output files
+------------
+
+    | **1) TICs_raw.pdf (Total Ion Chromatogram) :**
+
+    .. image:: BPCs_raw.pdf
+
+    | **2) BPCs_raw.pdf (Base Peak Chromatograms) :**
+
+    .. image:: TICs_raw.pdf
+
+    | **3) GCMS_EIC.pdf (Extracted Ion Chromatogram) :**
+
+    .. image:: GCMS_EIC.pdf
+
+
+---------------------------------------------------
+
+Changelog/News
+--------------
+**Version 1.0 - 20/05/2019**
+
+- NEW: new tool extract from previous metaMS_runGC tool
+
+    </help>
+
+    <citations>
+        <citation type="doi">10.1016/j.jchromb.2014.02.051</citation>
+        <citation type="doi">10.1093/bioinformatics/btu813</citation>
+    </citations>
+
+</tool>
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