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changeset 1:107a3de94c05 draft

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Uploaded
author lecorguille
date Fri, 08 Jan 2016 09:53:56 -0500
parents 30b01bcefda4
children 25786044e8b8
files Makefile abims_xcms_fillPeaks.xml planemo.sh repository_dependencies.xml static/.svn/entries static/images/.svn/entries static/images/.svn/prop-base/xcms_fillpeaks_workflow.png.svn-base static/images/.svn/text-base/xcms_fillpeaks_workflow.png.svn-base test-data/.svn/entries test-data/.svn/prop-base/xset.group.retcor.group.RData.svn-base test-data/.svn/prop-base/xset.group.retcor.group.fillPeaks.RData.svn-base test-data/.svn/text-base/xset.group.retcor.group.RData.svn-base test-data/.svn/text-base/xset.group.retcor.group.fillPeaks.RData.svn-base 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 18 files changed, 304 insertions(+), 35 deletions(-) [+]
line wrap: on
line diff
--- a/Makefile	Fri Aug 07 05:35:50 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-# USAGE: make [install|clean]
-
-# -------- VARIABLE --------
-
-OBJ=xcms_fillpeaks.tgz
-DEP=abims_xcms_fillPeaks.xml tool_dependencies.xml repository_dependencies.xml static test-data
-
-
-# ------------------------
-
-all: $(OBJ)
-
-$(OBJ): $(DEP)
-	tar --exclude=".svn" -zchf $@ $^
-
-# ------------------------
-
-install: $(OBJ)
-	mv *.tgz ~
-
-clean:
-	rm *.tgz
-
--- a/abims_xcms_fillPeaks.xml	Fri Aug 07 05:35:50 2015 -0400
+++ b/abims_xcms_fillPeaks.xml	Fri Jan 08 09:53:56 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="2.0.4">
 
     <description>Integrate the signal in the region of that peak group not represented and create a new peak</description>
 
@@ -13,9 +13,25 @@
         <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
@@ -172,7 +202,7 @@
     | **xset.fillPeaks.RData: RData file**
 
 
-    </help>
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1021/ac051437y</citation>
--- a/planemo.sh	Fri Aug 07 05:35:50 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-planemo shed_init -f --name=xcms_fillpeaks --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Integrate areas of missing peaks" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nFor each sample, identify peak groups where that sample is not represented. For each of those peak groups, integrate the signal in the region of that peak group and create a new peak.\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics"
--- a/repository_dependencies.xml	Fri Aug 07 05:35:50 2015 -0400
+++ b/repository_dependencies.xml	Fri Jan 08 09:53:56 2016 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
 <repositories>
-    <repository changeset_revision="9ed593071db2" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="5527da68412e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     <repository changeset_revision="bff835d58914" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/.svn/entries	Fri Jan 08 09:53:56 2016 -0500
@@ -0,0 +1,31 @@
+10
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+dir
+157
+svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_fillpeaks/static
+svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo
+
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+images
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/.svn/entries	Fri Jan 08 09:53:56 2016 -0500
@@ -0,0 +1,62 @@
+10
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+dir
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+svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_fillpeaks/static/images
+svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/.svn/prop-base/xcms_fillpeaks_workflow.png.svn-base	Fri Jan 08 09:53:56 2016 -0500
@@ -0,0 +1,9 @@
+K 14
+svn:executable
+V 1
+*
+K 13
+svn:mime-type
+V 24
+application/octet-stream
+END
Binary file static/images/.svn/text-base/xcms_fillpeaks_workflow.png.svn-base has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/entries	Fri Jan 08 09:53:56 2016 -0500
@@ -0,0 +1,96 @@
+10
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+svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_fillpeaks/test-data
+svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/prop-base/xset.group.retcor.group.RData.svn-base	Fri Jan 08 09:53:56 2016 -0500
@@ -0,0 +1,5 @@
+K 13
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+V 24
+application/octet-stream
+END
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/prop-base/xset.group.retcor.group.fillPeaks.RData.svn-base	Fri Jan 08 09:53:56 2016 -0500
@@ -0,0 +1,5 @@
+K 13
+svn:mime-type
+V 24
+application/octet-stream
+END
Binary file test-data/.svn/text-base/xset.group.retcor.group.RData.svn-base has changed
Binary file test-data/.svn/text-base/xset.group.retcor.group.fillPeaks.RData.svn-base has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log.txt	Fri Jan 08 09:53:56 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	Fri Aug 07 05:35:50 2015 -0400
+++ b/tool_dependencies.xml	Fri Jan 08 09:53:56 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="1ca39eb16186" 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" />
+        <repository changeset_revision="745fc3cb412e" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>