--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_plot_chromatogram.xml	Tue Sep 18 16:06:05 2018 -0400
@@ -0,0 +1,113 @@
+<tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0">
+    <description>Plots base peak intensity chromatogram (BPI) and total ion current chromatogram (TIC) from MSnbase or xcms experiment(s)</description>
+
+    <macros>
+        <import>macros.xml</import>
+        <import>macros_xcms.xml</import>
+    </macros>
+
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+
+    <command><![CDATA[
+        @COMMAND_RSCRIPT@//xcms_plot_chromatogram.r
+
+        images 'c("${"\",\"".join(map(str, $images))}")'
+
+        #if str($sampleMetadata) != 'None':
+            sampleMetadata '$sampleMetadata'
+        #end if
+
+        @COMMAND_FILE_LOAD@
+    ]]></command>
+
+    <inputs>
+        <param name="images" type="data" format="rdata.msnbase.raw,rdata.xcms.findchrompeaks,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" multiple="true" />
+        <param name="sampleMetadata" label="Sample metadata file " format="tabular" type="data" optional="true" help="Must contain at least one column with the sample id and one column with the sample class"/>
+
+        <expand macro="input_file_load"/>
+    </inputs>
+
+    <outputs>
+        <data name="ticsPdf" format="pdf"  label="TICs.pdf" from_work_dir="TICs.pdf"/>
+        <data name="bpisPdf" format="pdf" label="BPIs.pdf" from_work_dir="BPIs.pdf" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="images" value="faahKO-single.xset.merged.group.retcor.RData" ftype="rdata"/>
+            <expand macro="test_file_load_single"/>
+            <param name="sampleMetadata" value="sampleMetadata.tab" ftype="tabular"/>
+            <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
+            <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
+        </test>
+        <!-- DISABLE FOR TRAVIS
+        <test>
+            <param name="images" value="ko15-raw.RData,ko16-raw.RData,wt15-raw.RData,wt16-raw.RData" ftype="rdata"/>
+            <expand macro="test_file_load_single"/>
+            <output name="ticsPdf" value="TICs.pdf" ftype="pdf" compare="sim_size" delta="600" />
+            <output name="bpisPdf" value="BPIs.pdf" ftype="pdf" compare="sim_size" delta="600" />
+        </test>
+        -->
+    </tests>
+
+    <help><![CDATA[
+
+@HELP_AUTHORS@
+
+======================
+xcms plot chromatogram
+======================
+
+-----------
+Description
+-----------
+
+This tool will plot Base Peak Intensity chromatogram (BPI) and Total Ion Current chromatogram (TIC) from xcms experiments.
+
+
+-----------------
+Workflow position
+-----------------
+
+**Upstream tools**
+
+=========================== ======================== ==============================
+Name                        Output file              Format
+=========================== ======================== ==============================
+MSnbase.readMSData          ``*``.raw.RData          rdata.msnbase.raw
+--------------------------- ------------------------ ------------------------------
+xcms.findChromPeaks         ``*``.raw.xset.RData     rdata.xcms.findchrompeaks
+--------------------------- ------------------------ ------------------------------
+xcms.findChromPeaks Merger  xset.merged.RData        rdata.xcms.retcor
+--------------------------- ------------------------ ------------------------------
+xcms.adjustRtime            ``*``.adjustRtime.RData  rdata.xcms.retcor
+=========================== ======================== ==============================
+
+.. image:: xcms_plot_chromatogram_workflow.png
+
+---------------------------------------------------
+
+------------
+Output files
+------------
+
+**Total Ion Current (TIC) chromatogram**
+    | Sum of intensity (Y) of all ions detected at each retention time (X)
+
+**Base Peak Intensity Chromatogram (BPI)**
+    | Sum of intensity (Y) of the most intense peaks at each retention time (X)
+
+---------------------------------------------------
+
+Changelog/News
+--------------
+
+**Version 3.0.0.0 - 07/03/2018**
+
+- NEW: This new tool will plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience. It will replace those created by xcmsSet and retcor tools.
+
+    ]]></help>
+
+    <expand macro="citation" />
+</tool>