diff xcms_plot_chromatogram.xml @ 2:e6fdadaf039e draft

planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f01148783819c37e474790dbd56619862960448a

--- a/xcms_plot_chromatogram.xml	Thu Mar 08 05:52:12 2018 -0500
+++ b/xcms_plot_chromatogram.xml	Tue Apr 03 11:37:40 2018 -0400
@@ -1,39 +1,53 @@
 <tool id="xcms_plot_chromatogram" name="xcms plot chromatogram" version="@WRAPPER_VERSION@.0">
-    <description>Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from xcms experience</description>
+    <description>Plot base peak intensity chromatogram (BPI) and total ion chromatogram (TIC) from MSnbase or xcms experience(s)</description>
 
     <macros>
         <import>macros.xml</import>
+        <import>macros_xcms.xml</import>
     </macros>
 
     <expand macro="requirements"/>
     <expand macro="stdio"/>
 
     <command><![CDATA[
-        @COMMAND_XCMS_SCRIPT@/xcms_plot_chromatogram.r
+        @COMMAND_RSCRIPT@//xcms_plot_chromatogram.r
+
+        images 'c("${"\",\"".join(map(str, $images))}")'
 
-        image '$image'
+        #if str($sampleMetadata) != 'None':
+            sampleMetadata '$sampleMetadata'
+        #end if
 
         @COMMAND_FILE_LOAD@
     ]]></command>
 
     <inputs>
-        <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata" label="@INPUT_IMAGE_LABEL@" help="@INPUT_IMAGE_HELP@ from: findChromPeaks, groupChromPeaks or adjustRtime" />
+        <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="${image.name[:-6]}.TICs.pdf" from_work_dir="TICs.pdf"/>
-        <data name="bpisPdf" format="pdf" label="${image.name[:-6]}.BPIs.pdf" from_work_dir="BPIs.pdf" />
+        <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="image" value="faahKO-single.xset.merged.group.retcor.RData"/>
+            <param name="images" value="faahKO-single.xset.merged.group.retcor.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>
+        <!-- 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[
@@ -57,16 +71,19 @@
 
 **Upstream tools**
 
-========================= ================= =================== ==========
-Name                      output file       format              parameter
-========================= ================= =================== ==========
-xcms.xcmsSet              xset.RData        rdata.xcms.raw      RData file
-------------------------- ----------------- ------------------- ----------
-xcms.retcor               xset.RData        rdata.xcms.retcor   RData file
-========================= ================= =================== ==========
+========================= ================= ============================== ==========
+Name                      output file       format                         parameter
+========================= ================= ============================== ==========
+MSnbase readMSData        raw.RData         rdata.msnbase.raw              RData file
+------------------------- ----------------- ------------------------------ ----------
+xcms.xcmsSet              xset.RData        rdata.xcms.findchrompeaks      RData file
+------------------------- ----------------- ------------------------------ ----------
+xcms.retcor               xset.RData        rdata.xcms.retcor              RData file
+========================= ================= ============================== ==========
 
 .. image:: xcms_plot_chromatogram_workflow.png
 
+---------------------------------------------------
 
 ------------
 Output files
@@ -85,7 +102,7 @@
 
 **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 the one created by xcmsSet and retcor tools.
+- 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>