# HG changeset patch
# User lecorguille
# Date 1450886677 18000
# Node ID 2f5b78be1dd6c8d4bd70d31f0dfd979b3de65b6d
# Parent  1bad16e5e4ae069007106aa490e1a8afff22e8d8
Uploaded

diff -r 1bad16e5e4ae -r 2f5b78be1dd6 Makefile
--- a/Makefile	Fri Aug 07 07:48:57 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-# USAGE: make [install|clean]
-
-# -------- VARIABLE --------
-
-OBJ=xcms_set.tgz
-DEP=abims_xcms_xcmsSet.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 1bad16e5e4ae -r 2f5b78be1dd6 abims_xcms_xcmsSet.xml
--- a/abims_xcms_xcmsSet.xml	Fri Aug 07 07:48:57 2015 -0400
+++ b/abims_xcms_xcmsSet.xml	Wed Dec 23 11:04:37 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.2">
+<tool id="abims_xcms_xcmsSet" name="xcms.xcmsSet" version="2.0.5">
     
     <description>Filtration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis </description>
     
@@ -13,7 +13,7 @@
         <exit_code range="1:" level="fatal" />
     </stdio>
     
-    <command>
+    <command><![CDATA[
         xcms.r
         #if $inputs.input == "lib":
             library $__app__.config.user_library_import_dir/$__user_email__/$inputs.library
@@ -22,6 +22,12 @@
         #end if
 
         xfunction xcmsSet
+
+        xsetRdataOutput $xsetRData
+        sampleMetadataOutput $sampleMetadata
+        ticspdf $ticsRawPdf
+        bicspdf $bpcsRawPdf
+
         ## profmethod $profmethod 
         nSlaves \${GALAXY_SLOTS:-1} method $methods.method 
         #if $methods.method == "centWave":
@@ -29,14 +35,14 @@
             peakwidth "c($methods.peakwidth)"
         #if $methods.options_scanrange.option == "show":
                 scanrange "c($methods.options_scanrange.scanrange)"
-            #end if 
-            #if $methods.options_c.option == "show":
-                mzdiff $methods.options_c.mzdiff
-                snthresh $methods.options_c.snthresh
-                integrate $methods.options_c.integrate
-                noise $methods.options_c.noise
-                prefilter "c($methods.options_c.prefilter)"
-            #end if
+        #end if 
+        #if $methods.options_c.option == "show":
+            mzdiff $methods.options_c.mzdiff
+            snthresh $methods.options_c.snthresh
+            integrate $methods.options_c.integrate
+            noise $methods.options_c.noise
+            prefilter "c($methods.options_c.prefilter)"
+        #end if
         #elif $methods.method == "matchedFilter":
             step $methods.step
             fwhm $methods.fwhm
@@ -56,13 +62,12 @@
             scales "c($methods.scales)"
             SNR.method "$methods.SNR_method"
         #end if
-        &amp;&amp; (mv xcmsSet.RData $xsetRData;
-        mv sampleMetadata.tsv $sampleMetadata;
-        mv TICs_raw.pdf $ticsRawPdf;
-        mv BPCs_raw.pdf $bpcsRawPdf;
-        mv xset.log $log);
-        cat $log
-    </command>
+        ;
+        return=\$?;
+        mv log.txt $log;
+        cat $log;
+        sh -c "exit \$return"
+    ]]></command>
     
     <inputs>
 
@@ -113,6 +118,8 @@
                             <validator type="empty_field"/> 
                         </param>
                     </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
                         
                 <conditional name="options_c">
@@ -130,6 +137,8 @@
                         <param name="prefilter" type="text" value="3,100" label="Prefilter step for the first phase" help="[prefilter] Separate by coma k,I. Mass traces are only retained if they contain at least ‘k’ peaks with intensity >= ‘I’"/>
                         <param name="noise" type="integer" value="0" label="Noise filter" help="[noise] optional argument which is useful for data that was centroided without any intensity threshold, centroids with intensity smaller than ‘noise’ are omitted from ROI detection"/>
                     </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
             </when>
 
@@ -153,6 +162,8 @@
                         <param name="mzdiff" type="text" size="20" value="0.8-step*steps" label="m/z difference" help="min m/z difference for peaks with overlapping RT " />
 -->
                     </when>
+                    <when value="hide">
+                    </when>
                 </conditional>
             </when>
 
@@ -190,15 +201,24 @@
             <param name="methods.options_m.max" value="50" />
             <param name="methods.options_m.snthresh" value="1" />
             <param name="methods.options_m.steps" value="2" />
-            <output name="xsetRData" file="xset.RData" />
-            <output name="sampleMetadata" file="sampleMetadata.tsv" />
-            <output name="ticsRawPdf" file="xset.TICs_raw.pdf" />
-            <output name="bpcsRawPdf" file="xset.BPCs_raw.pdf" />
-            <output name="log" file="xset.log.txt" />
+            <!--<output name="xsetRData" file="xset.RData" />-->
+            <!--<output name="sampleMetadata" file="sampleMetadata.tsv" />-->
+            <!--<output name="ticsRawPdf" file="xset.TICs_raw.pdf" />-->
+            <!--<output name="bpcsRawPdf" file="xset.BPCs_raw.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: 0" />
+                    <has_text text="Sample classes: bio, blank" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     
-    <help>
+    <help><![CDATA[
 
 .. class:: infomark
 
@@ -392,7 +412,7 @@
 .. image:: xcms_tics.png
 
 
-    </help>
+    ]]></help>
 
 
     <citations>
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 planemo.sh
--- a/planemo.sh	Fri Aug 07 07:48:57 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-planemo shed_init -f --name=xcms_xcms_set --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - peaks calling in NetCDF/mzXML files" --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\nFiltration and Peak Identification using xcmsSet function from xcms R package to preprocess LC/MS data for relative quantification and statistical analysis\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 1bad16e5e4ae -r 2f5b78be1dd6 static/.svn/entries
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/.svn/entries	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,31 @@
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diff -r 1bad16e5e4ae -r 2f5b78be1dd6 static/images/.svn/entries
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/.svn/entries	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,96 @@
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diff -r 1bad16e5e4ae -r 2f5b78be1dd6 static/images/.svn/prop-base/XCMS_Galaxy_workflow.png.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/.svn/prop-base/XCMS_Galaxy_workflow.png.svn-base	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,9 @@
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diff -r 1bad16e5e4ae -r 2f5b78be1dd6 static/images/.svn/prop-base/xcms_tics.png.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/static/images/.svn/prop-base/xcms_tics.png.svn-base	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,9 @@
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diff -r 1bad16e5e4ae -r 2f5b78be1dd6 static/images/.svn/text-base/XCMS_Galaxy_workflow.png.svn-base
Binary file static/images/.svn/text-base/XCMS_Galaxy_workflow.png.svn-base has changed
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 static/images/.svn/text-base/xcms_tics.png.svn-base
Binary file static/images/.svn/text-base/xcms_tics.png.svn-base has changed
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/entries
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/entries	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,232 @@
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diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/prop-base/sacuri.zip.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/prop-base/sacuri.zip.svn-base	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,5 @@
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diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/prop-base/xset.RData.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/prop-base/xset.RData.svn-base	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,5 @@
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diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/prop-base/xset.TICs_raw.pdf.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/prop-base/xset.TICs_raw.pdf.svn-base	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,5 @@
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diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/text-base/sacuri.zip.svn-base
Binary file test-data/.svn/text-base/sacuri.zip.svn-base has changed
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/text-base/sampleMetadata.tsv.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/text-base/sampleMetadata.tsv.svn-base	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,10 @@
+sampleMetadata	class	polarity
+HU_neg_028	bio	negative
+HU_neg_060	bio	negative
+HU_neg_051	bio	negative
+HU_neg_017	bio	negative
+HU_neg_034	bio	negative
+Blanc09	blank	negative
+Blanc06	blank	negative
+Blanc12	blank	negative
+Blanc04	blank	negative
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/text-base/xset.BPCs_raw.pdf.svn-base
Binary file test-data/.svn/text-base/xset.BPCs_raw.pdf.svn-base has changed
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/text-base/xset.RData.svn-base
Binary file test-data/.svn/text-base/xset.RData.svn-base has changed
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/text-base/xset.TICs_raw.pdf.svn-base
Binary file test-data/.svn/text-base/xset.TICs_raw.pdf.svn-base has changed
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/.svn/text-base/xset.log.txt.svn-base
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/.svn/text-base/xset.log.txt.svn-base	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,56 @@
+	PACKAGE INFO
+parallel	3.1.1
+BiocGenerics	0.12.1
+Biobase	2.26.0
+Rcpp	0.11.5
+mzR	2.0.0
+igraph	0.7.1
+xcms	1.42.0
+snow	0.3.13
+batch	1.1.4
+
+
+	ARGUMENTS INFO
+zipfile	/w/galaxy/galaxy4metabolomics/galaxy-dist/database/files/041/dataset_41794.dat
+xfunction	xcmsSet
+nSlaves	8
+method	matchedFilter
+step	0.01
+fwhm	4
+max	50
+snthresh	1
+steps	2
+
+
+	INFILE PROCESSING INFO
+
+
+	MAIN PROCESSING INFO
+Starting snow cluster with 8 local sockets.
+Detecting features in file # 1 : HU_neg_028.mzXML 
+Detecting features in file # 2 : HU_neg_060.mzXML 
+Detecting features in file # 3 : HU_neg_051.mzXML 
+Detecting features in file # 4 : HU_neg_017.mzXML 
+Detecting features in file # 5 : HU_neg_034.mzXML 
+Detecting features in file # 6 : Blanc09.mzXML 
+Detecting features in file # 7 : Blanc06.mzXML 
+Detecting features in file # 8 : Blanc12.mzXML 
+Detecting features in file # 9 : Blanc04.mzXML 
+
+
+	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: 0 
+Sample classes: bio, blank 
+
+Profile settings: method = bin
+                  step = 0.01
+
+Memory usage: 13.8 MB
+
+
+	DONE
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/log.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/log.txt	Wed Dec 23 11:04:37 2015 -0500
@@ -0,0 +1,56 @@
+	PACKAGE INFO
+parallel	3.1.1
+BiocGenerics	0.12.1
+Biobase	2.26.0
+Rcpp	0.11.5
+mzR	2.0.0
+igraph	0.7.1
+xcms	1.42.0
+snow	0.3.13
+batch	1.1.4
+
+
+	ARGUMENTS INFO
+zipfile	/w/galaxy/galaxy4metabolomics/galaxy-dist/database/files/041/dataset_41794.dat
+xfunction	xcmsSet
+nSlaves	8
+method	matchedFilter
+step	0.01
+fwhm	4
+max	50
+snthresh	1
+steps	2
+
+
+	INFILE PROCESSING INFO
+
+
+	MAIN PROCESSING INFO
+Starting snow cluster with 8 local sockets.
+Detecting features in file # 1 : HU_neg_028.mzXML 
+Detecting features in file # 2 : HU_neg_060.mzXML 
+Detecting features in file # 3 : HU_neg_051.mzXML 
+Detecting features in file # 4 : HU_neg_017.mzXML 
+Detecting features in file # 5 : HU_neg_034.mzXML 
+Detecting features in file # 6 : Blanc09.mzXML 
+Detecting features in file # 7 : Blanc06.mzXML 
+Detecting features in file # 8 : Blanc12.mzXML 
+Detecting features in file # 9 : Blanc04.mzXML 
+
+
+	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: 0 
+Sample classes: bio, blank 
+
+Profile settings: method = bin
+                  step = 0.01
+
+Memory usage: 13.8 MB
+
+
+	DONE
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 test-data/xset.log.txt
--- a/test-data/xset.log.txt	Fri Aug 07 07:48:57 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-	PACKAGE INFO
-parallel	3.1.1
-BiocGenerics	0.12.1
-Biobase	2.26.0
-Rcpp	0.11.5
-mzR	2.0.0
-igraph	0.7.1
-xcms	1.42.0
-snow	0.3.13
-batch	1.1.4
-
-
-	ARGUMENTS INFO
-zipfile	/w/galaxy/galaxy4metabolomics/galaxy-dist/database/files/041/dataset_41794.dat
-xfunction	xcmsSet
-nSlaves	8
-method	matchedFilter
-step	0.01
-fwhm	4
-max	50
-snthresh	1
-steps	2
-
-
-	INFILE PROCESSING INFO
-
-
-	MAIN PROCESSING INFO
-Starting snow cluster with 8 local sockets.
-Detecting features in file # 1 : HU_neg_028.mzXML 
-Detecting features in file # 2 : HU_neg_060.mzXML 
-Detecting features in file # 3 : HU_neg_051.mzXML 
-Detecting features in file # 4 : HU_neg_017.mzXML 
-Detecting features in file # 5 : HU_neg_034.mzXML 
-Detecting features in file # 6 : Blanc09.mzXML 
-Detecting features in file # 7 : Blanc06.mzXML 
-Detecting features in file # 8 : Blanc12.mzXML 
-Detecting features in file # 9 : Blanc04.mzXML 
-
-
-	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: 0 
-Sample classes: bio, blank 
-
-Profile settings: method = bin
-                  step = 0.01
-
-Memory usage: 13.8 MB
-
-
-	DONE
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Aug 07 07:48:57 2015 -0400
+++ b/tool_dependencies.xml	Wed Dec 23 11:04:37 2015 -0500
@@ -1,10 +1,10 @@
 <?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="68077fb03d75" 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" />
diff -r 1bad16e5e4ae -r 2f5b78be1dd6 xcms_set.tgz
Binary file xcms_set.tgz has changed