# HG changeset patch
# User lecorguille
# Date 1452264758 18000
# Node ID f42bd3de6aad9cdd0b1d7b8e9e5b392efce07239
# Parent  ad95fea4015efb29d5c9410d1714cfcb45fed3fc
Uploaded

diff -r ad95fea4015e -r f42bd3de6aad Makefile
--- a/Makefile	Fri Aug 07 05:34:26 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-# USAGE: make [install|clean]
-
-# -------- VARIABLE --------
-
-OBJ=xcms_retcor.tgz
-DEP=abims_xcms_retcor.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
-
diff -r ad95fea4015e -r f42bd3de6aad abims_xcms_retcor.xml
--- a/abims_xcms_retcor.xml	Fri Aug 07 05:34:26 2015 -0400
+++ b/abims_xcms_retcor.xml	Fri Jan 08 09:52:38 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.2">
+<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.4">
 
     <description>Retention Time Correction using retcor function from xcms R package </description>
 
@@ -13,9 +13,17 @@
         <exit_code range="1:" level="fatal" />
     </stdio>
 
-    <command>
+    <command><![CDATA[
         xcms.r 
-        image $image xfunction retcor method $methods.method
+        image $image 
+        xfunction retcor 
+
+        xsetRdataOutput $xsetRData
+        ticspdf $ticsCorPdf
+        bicspdf $bpcsCorPdf
+        rplotspdf $rplotsPdf
+
+        method $methods.method
         #if $methods.method == "obiwarp":
             profStep $methods.profStep
         #else
@@ -28,13 +36,16 @@
                 plottype $methods.options.plottype
             #end if
         #end if
-        &amp;&amp; ( mv retcor.RData $xsetRData;
-        mv TICs_corrected.pdf $ticsCorPdf ;
-        mv BPCs_corrected.pdf $bpcsCorPdf ;
-        mv Rplots.pdf $rplotsPdf 2> /dev/null);
-        cat xset.log; 
+        #if $zip_file:
+            zipfile $zip_file
+        #end if
+        ;
+        return=\$?;
+        mv log.txt $log;
+        cat $log;
+        sh -c "exit \$return"
         
-    </command>
+    ]]></command>
 
     <inputs>
         <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" />
@@ -61,22 +72,24 @@
                     <when value="show">
                         <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/>
                         
-            <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
-                        <option value="gaussian" selected="true">gaussian</option>
-                        <option value="symmetric">symmetric</option>
-                    </param>
+                        <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal">
+                            <option value="gaussian" selected="true">gaussian</option>
+                            <option value="symmetric">symmetric</option>
+                        </param>
 
-            <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
+                        <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density">
                             <option value="none" selected="true">none</option>
                             <option value="deviation">deviation</option>
                             <option value="mdevden">mdevden</option>
                         </param>
                     </when>
-            <when value="hide">
-            </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
             </when>
         </conditional>
+        <!-- To pass planemo test -->
+        <param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" />
     </inputs>
 
     <outputs>
@@ -89,6 +102,7 @@
         </data>
         <data name="ticsCorPdf"   format="pdf"  label="${image.name[:-6]}.retcor.TICs_corrected.pdf" />
         <data name="bpcsCorPdf"   format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" />
+        <data name="log" format="txt" label="xset.log.txt"  hidden="true" />
     </outputs>
     
     <tests>
@@ -102,14 +116,25 @@
             <param name="methods.options.span" value="0.2"/>
             <param name="methods.options.family" value="gaussian"/>
             <param name="methods.options.plottype" value="deviation"/>
-            <output name="xsetRData" file="xset.group.retcor.RData" />
-            <output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />
-            <output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />
-            <output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />
+            <param name="zip_file" value="sacuri.zip"/>
+            <!--<output name="xsetRData" file="xset.group.retcor.RData" />-->
+            <!--<output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />-->
+            <!--<output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />-->
+            <!--<output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />-->
+            <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: 135846 (about 15094 per sample)" />
+                    <has_text text="Peak Groups: 0" />
+                    <has_text text="Sample classes: bio, blank" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
 
-    <help>
+    <help><![CDATA[
 
         
 .. class:: infomark
@@ -266,7 +291,7 @@
 
 .. image:: xcms_retcor.png
 
-    </help>
+    ]]></help>
 
     <citations>
         <citation type="doi">10.1021/ac051437y</citation>
diff -r ad95fea4015e -r f42bd3de6aad planemo.sh
--- a/planemo.sh	Fri Aug 07 05:34:26 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-planemo shed_init -f --name=xcms_retcor --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples" --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\nRetention Time Correction using retcor function from xcms R package\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics"
diff -r ad95fea4015e -r f42bd3de6aad repository_dependencies.xml
--- a/repository_dependencies.xml	Fri Aug 07 05:34:26 2015 -0400
+++ b/repository_dependencies.xml	Fri Jan 08 09:52:38 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>
diff -r ad95fea4015e -r f42bd3de6aad static/.svn/entries
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/.svn/entries	Fri Jan 08 09:52:38 2016 -0500
@@ -0,0 +1,31 @@
+10
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+svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo
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diff -r ad95fea4015e -r f42bd3de6aad static/images/.svn/entries
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/.svn/entries	Fri Jan 08 09:52:38 2016 -0500
@@ -0,0 +1,96 @@
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diff -r ad95fea4015e -r f42bd3de6aad static/images/.svn/prop-base/xcms_retcor.png.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/.svn/prop-base/xcms_retcor.png.svn-base	Fri Jan 08 09:52:38 2016 -0500
@@ -0,0 +1,9 @@
+K 14
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+V 1
+*
+K 13
+svn:mime-type
+V 24
+application/octet-stream
+END
diff -r ad95fea4015e -r f42bd3de6aad static/images/.svn/prop-base/xcms_retcor_workflow.png.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/.svn/prop-base/xcms_retcor_workflow.png.svn-base	Fri Jan 08 09:52:38 2016 -0500
@@ -0,0 +1,9 @@
+K 14
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+V 1
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+K 13
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+END
diff -r ad95fea4015e -r f42bd3de6aad static/images/.svn/text-base/xcms_retcor.png.svn-base
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diff -r ad95fea4015e -r f42bd3de6aad static/images/.svn/text-base/xcms_retcor_workflow.png.svn-base
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diff -r ad95fea4015e -r f42bd3de6aad test-data/.svn/entries
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/entries	Fri Jan 08 09:52:38 2016 -0500
@@ -0,0 +1,198 @@
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diff -r ad95fea4015e -r f42bd3de6aad test-data/.svn/prop-base/xset.group.RData.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/prop-base/xset.group.RData.svn-base	Fri Jan 08 09:52:38 2016 -0500
@@ -0,0 +1,5 @@
+K 13
+svn:mime-type
+V 24
+application/octet-stream
+END
diff -r ad95fea4015e -r f42bd3de6aad test-data/.svn/prop-base/xset.group.retcor.BPCs_corrected.pdf.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/prop-base/xset.group.retcor.BPCs_corrected.pdf.svn-base	Fri Jan 08 09:52:38 2016 -0500
@@ -0,0 +1,5 @@
+K 13
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+V 24
+application/octet-stream
+END
diff -r ad95fea4015e -r f42bd3de6aad test-data/.svn/prop-base/xset.group.retcor.RData.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/prop-base/xset.group.retcor.RData.svn-base	Fri Jan 08 09:52:38 2016 -0500
@@ -0,0 +1,5 @@
+K 13
+svn:mime-type
+V 24
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diff -r ad95fea4015e -r f42bd3de6aad test-data/.svn/text-base/xset.group.RData.svn-base
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diff -r ad95fea4015e -r f42bd3de6aad test-data/.svn/text-base/xset.group.retcor.BPCs_corrected.pdf.svn-base
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diff -r ad95fea4015e -r f42bd3de6aad test-data/.svn/text-base/xset.group.retcor.RData.svn-base
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diff -r ad95fea4015e -r f42bd3de6aad test-data/.svn/text-base/xset.group.retcor.TICs_corrected.pdf.svn-base
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diff -r ad95fea4015e -r f42bd3de6aad test-data/log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log.txt	Fri Jan 08 09:52:38 2016 -0500
@@ -0,0 +1,52 @@
+	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
+image	test-data/xset.group.RData
+xfunction	retcor
+xsetRdataOutput	test-data/xset.group.retcor.RData
+ticspdf	xset.group.retcor.TICs_corrected.pdf
+bicspdf	xset.group.retcor.BPCs_corrected.pdf
+rplotspdf	xset.group.retcor.Rplots.pdf
+method	obiwarp
+profStep	1
+zipfile	test-data/sacuri.zip
+
+
+	INFILE PROCESSING INFO
+
+
+	ARGUMENTS PROCESSING INFO
+
+
+	MAIN PROCESSING INFO
+center sample:  HU_neg_060 
+Processing: HU_neg_028  HU_neg_051  HU_neg_017  HU_neg_034  Blanc09  Blanc06  Blanc12  Blanc04  
+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: 135846 (about 15094 per sample)
+Peak Groups: 0 
+Sample classes: bio, blank 
+
+Profile settings: method = bin
+                  step = 0.01
+
+Memory usage: 13.8 MB
+
+
+	DONE
diff -r ad95fea4015e -r f42bd3de6aad test-data/sacuri.zip
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diff -r ad95fea4015e -r f42bd3de6aad test-data/xset.group.RData
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diff -r ad95fea4015e -r f42bd3de6aad test-data/xset.group.retcor.BPCs_corrected.pdf
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diff -r ad95fea4015e -r f42bd3de6aad test-data/xset.group.retcor.RData
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diff -r ad95fea4015e -r f42bd3de6aad test-data/xset.group.retcor.Rplots.pdf
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diff -r ad95fea4015e -r f42bd3de6aad test-data/xset.group.retcor.TICs_corrected.pdf
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diff -r ad95fea4015e -r f42bd3de6aad tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Aug 07 05:34:26 2015 -0400
+++ b/tool_dependencies.xml	Fri Jan 08 09:52:38 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>