Mercurial > repos > lecorguille > xcms_group

changeset 1:df264428a5e1 draft

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Uploaded
author lecorguille
date Mon, 04 Jan 2016 08:33:29 -0500
parents 2a104ea58d12
children 1e1d5af9684a
files abims_xcms_group.xml test-data/log.txt test-data/xset.group.RData tool_dependencies.xml
diffstat 4 files changed, 86 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/abims_xcms_group.xml	Fri Aug 07 06:04:38 2015 -0400
+++ b/abims_xcms_group.xml	Mon Jan 04 08:33:29 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_group" name="xcms.group" version="2.0.2">
+<tool id="abims_xcms_group" name="xcms.group" version="2.0.4">
 
     <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description>
 
@@ -13,9 +13,15 @@
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command>
+    <command><![CDATA[
         xcms.r 
-        xfunction group image $image method $methods.method sleep 0.001 
+        xfunction group 
+        image $image 
+
+        xsetRdataOutput $xsetRData
+        rplotspdf $rplotsPdf
+
+        method $methods.method sleep 0.001 
         #if $methods.method == "density":
             ## minsamp $methods.minsamp 
             minfrac $methods.minfrac 
@@ -35,12 +41,13 @@
             rtCheck $methods.rtCheck
             kNN $methods.kNN
         #end if
-        &amp;&amp; (
-        mv group.RData $xsetRData;
-        mv Rplots.pdf $rplotsPdf
-        );
-        cat xset.log
-   </command> 
+        ;
+        return=\$?;
+        mv log.txt $log;
+        cat $log;
+        sh -c "exit \$return"
+        
+   ]]></command> 
 
     <inputs>
         <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
@@ -96,6 +103,7 @@
     <outputs>
         <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/>
         <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/>
+        <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
     </outputs>
 
     <tests>
@@ -107,13 +115,23 @@
             <param name="methods.mzwid" value="0.01"/>
             <param name="methods.density_options.option" value="show"/>
             <param name="methods.density_options.max" value="50"/>
-            <output name="xsetRData" file="xset.group.RData" />
-            <output name="rplotsPdf" file="xset.group.Rplots.pdf" />
+            <!--<output name="xsetRData" file="xset.group.RData" />-->
+            <!--<output name="rplotsPdf" file="xset.group.Rplots.pdf" />-->
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 9 samples" />
+                    <has_text text="Time range: 0.7-1140 seconds (0-19 minutes)" />
+                    <has_text text="Mass range: 50.0019-999.9863 m/z" />
+                    <has_text text="Peaks: 135846 (about 15094 per sample)" />
+                    <has_text text="Peak Groups: 6642" />
+                    <has_text text="Sample classes: bio, blank" />
+                </assert_contents>
+            </output>
          
         </test>
     </tests>
 
-    <help>
+    <help><![CDATA[
         
 .. class:: infomark
 
@@ -254,7 +272,7 @@
         :width: 700
 
 
-    </help>
+    ]]></help>
 
 
     <citations>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log.txt	Mon Jan 04 08:33:29 2016 -0500
@@ -0,0 +1,51 @@
+	PACKAGE INFO
+parallel	3.1.2
+BiocGenerics	0.14.0
+Biobase	2.28.0
+Rcpp	0.12.0
+mzR	2.2.2
+xcms	1.44.0
+snow	0.3.13
+batch	1.1.4
+
+
+	ARGUMENTS INFO
+xfunction	group
+image	test-data/xset.RData
+xsetRdataOutput	test-data/xset.group.RData
+rplotspdf	xset.group.Rplots.pdf
+method	density
+sleep	0.001
+minfrac	0.5
+bw	30
+mzwid	0.25
+
+
+	INFILE PROCESSING INFO
+
+
+	ARGUMENTS PROCESSING INFO
+
+
+	MAIN PROCESSING INFO
+112 175 237 300 362 425 487 550 612 675 737 800 862 925 987 
+null device 
+          1 
+
+
+	XSET OBJECT INFO
+An "xcmsSet" object with 9 samples
+
+Time range: 0.7-1140 seconds (0-19 minutes)
+Mass range: 50.0019-999.9863 m/z
+Peaks: 135846 (about 15094 per sample)
+Peak Groups: 6642 
+Sample classes: bio, blank 
+
+Profile settings: method = bin
+                  step = 0.01
+
+Memory usage: 15 MB
+
+
+	DONE
Binary file test-data/xset.group.RData has changed
--- a/tool_dependencies.xml	Fri Aug 07 06:04:38 2015 -0400
+++ b/tool_dependencies.xml	Mon Jan 04 08:33:29 2016 -0500
@@ -1,12 +1,12 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="R" version="3.1.2">
-        <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="73cd1d529330" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="xcms" version="1.44.0">
-        <repository changeset_revision="709473976109" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="8ea252413ed6" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="xcms_w4m_script" version="2.1">
-        <repository changeset_revision="af163ca0ac33" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="xcms_w4m_script" version="2.2.0">
+        <repository changeset_revision="e0d3e1caf5d9" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>