Mercurial > repos > lecorguille > xcms_fillpeaks

changeset 3:5a54397dbc97 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload
author lecorguille
date Mon, 22 Feb 2016 16:40:19 -0500
parents 5815e6e11f9b
children 2edfa5e1f719
files README.rst abims_xcms_fillPeaks.xml repository_dependencies.xml test-data/log.txt test-data/sacuri.zip test-data/xset.group.retcor.group.RData test-data/xset.group.retcor.group.fillPeaks.RData tool_dependencies.xml
diffstat 8 files changed, 134 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Mon Feb 22 16:40:19 2016 -0500
@@ -0,0 +1,19 @@
+
+Changelog/News
+--------------
+
+**Version 2.0.5 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+- UPDATE: refactoring to feed the new report tool
+
+
+**Version 2.0.2 - 02/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
--- a/abims_xcms_fillPeaks.xml	Tue Nov 24 06:26:14 2015 -0500
+++ b/abims_xcms_fillPeaks.xml	Mon Feb 22 16:40:19 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.2">
+<tool id="abims_xcms_fillPeaks" name="xcms.fillPeaks" version="2.0.5">
 
     <description>Integrate the signal in the region of that peak group not represented and create a new peak</description>
 
@@ -6,16 +6,32 @@
         <requirement type="package" version="3.1.2">R</requirement>
         <requirement type="binary">Rscript</requirement>
         <requirement type="package" version="1.44.0">xcms</requirement>
-        <requirement type="package" version="2.1">xcms_w4m_script</requirement>
+        <requirement type="package" version="2.2.0">xcms_w4m_script</requirement>
     </requirements>
     
     <stdio>
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command>
-        xcms.r xfunction fillPeaks image $image method $method &amp;&amp; mv fillPeaks.RData $xsetRData; cat xset.log
-    </command>
+    <command><![CDATA[
+        xcms.r 
+        xfunction fillPeaks 
+        image $image 
+
+        xsetRdataOutput $xsetRData
+
+        method $method
+
+        ###if $zip_file:
+        ##    zipfile $zip_file
+        ###end if
+        ;
+        return=\$?;
+        mv log.txt $log;
+        cat $log;
+        sh -c "exit \$return"
+        
+    ]]></command>
 
     <inputs>
         <param name="image" type="data" format="rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (group)" />
@@ -23,21 +39,35 @@
             <option value="chrom" selected="true">chrom</option>
             <option value="MSW" >MSW</option>
         </param>
+        <!-- To pass planemo test -->
+        <!--<param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />-->
     </inputs>
 
     <outputs>
         <data name="xsetRData" format="rdata.xcms.fillpeaks" label="${image.name[:-6]}.fillPeaks.RData" />
+        <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
     </outputs>
     
     <tests>
         <test>
             <param name="image" value="xset.group.retcor.group.RData"/>
             <param name="method" value="chrom"/>
-            <output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" />
+            <param name="zip_file" value="sacuri.zip"/>
+            <!--<output name="xsetRData" file="xset.group.retcor.group.fillPeaks.RData" />-->
+            <output name="log">
+                <assert_contents>
+                    <has_text text="object with 9 samples" />
+                    <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" />
+                    <has_text text="Mass range: 50.0019-999.9863 m/z" />
+                    <has_text text="Peaks: 157780 (about 17531 per sample)" />
+                    <has_text text="Peak Groups: 6761" />
+                    <has_text text="Sample classes: bio, blank" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
 
-    <help>
+    <help><![CDATA[
 
         
 .. class:: infomark
@@ -172,9 +202,28 @@
     | **xset.fillPeaks.RData: RData file**
 
 
+---------------------------------------------------
+
+Changelog/News
+--------------
+
+**Version 2.0.5 - 10/02/2016**
+
+- BUGFIX: better management of errors. Datasets remained green although the process failed
+
+- UPDATE: refactoring of internal management of inputs/outputs
+
+- UPDATE: refactoring to feed the new report tool
 
 
-    </help>
+**Version 2.0.2 - 02/06/2015**
+
+- IMPROVEMENT: new datatype/dataset formats (rdata.xcms.raw, rdata.xcms.group, rdata.xcms.retcor ...) will facilitate the sequence of tools and so avoid incompatibility errors.
+
+- IMPROVEMENT: parameter labels have changed to facilitate their reading.
+
+
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1021/ac051437y</citation>
--- a/repository_dependencies.xml	Tue Nov 24 06:26:14 2015 -0500
+++ b/repository_dependencies.xml	Mon Feb 22 16:40:19 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories>
-    <repository changeset_revision="12afb0ecb55f" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="7800ba9a4c1e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     <repository changeset_revision="d64562a4ebb3" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
 </repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log.txt	Mon Feb 22 16:40:19 2016 -0500
@@ -0,0 +1,55 @@
+	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	fillPeaks
+image	test-data/xset.group.retcor.group.RData
+xsetRdataOutput	test-data/xset.group.retcor.group.fillPeaks.RData
+method	chrom
+zipfile	test-data/sacuri.zip
+
+
+	INFILE PROCESSING INFO
+
+
+	ARGUMENTS PROCESSING INFO
+
+
+	MAIN PROCESSING INFO
+./sacuri/bio/HU_neg_028.mzXML 
+./sacuri/bio/HU_neg_060.mzXML 
+./sacuri/bio/HU_neg_051.mzXML 
+./sacuri/bio/HU_neg_017.mzXML 
+./sacuri/bio/HU_neg_034.mzXML 
+./sacuri/blank/Blanc09.mzXML 
+./sacuri/blank/Blanc06.mzXML 
+./sacuri/blank/Blanc12.mzXML 
+./sacuri/blank/Blanc04.mzXML 
+null device 
+          1 
+
+
+	XSET OBJECT INFO
+An "xcmsSet" object with 9 samples
+
+Time range: 0.7-1139.9 seconds (0-19 minutes)
+Mass range: 50.0019-999.9863 m/z
+Peaks: 157780 (about 17531 per sample)
+Peak Groups: 6761 
+Sample classes: bio, blank 
+
+Profile settings: method = bin
+                  step = 0.01
+
+Memory usage: 17.4 MB
+
+
+	DONE
Binary file test-data/sacuri.zip has changed
Binary file test-data/xset.group.retcor.group.RData has changed
Binary file test-data/xset.group.retcor.group.fillPeaks.RData has changed
--- a/tool_dependencies.xml	Tue Nov 24 06:26:14 2015 -0500
+++ b/tool_dependencies.xml	Mon Feb 22 16:40:19 2016 -0500
@@ -6,7 +6,7 @@
     <package name="xcms" version="1.44.0">
         <repository changeset_revision="4443617bdd85" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
-    <package name="xcms_w4m_script" version="2.1">
-        <repository changeset_revision="c94c8ef520c8" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
+    <package name="xcms_w4m_script" version="2.2.0">
+        <repository changeset_revision="115cf2b43a3c" name="package_xcms_w4m_script_2_2_0" owner="lecorguille" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>