# HG changeset patch # User lecorguille # Date 1456178873 18000 # Node ID 1245c04eebded21f15abf277a8b2ddb17f03efeb # Parent 89a8b5ff3e4420360e76b259140171b8bee916ad planemo upload diff -r 89a8b5ff3e44 -r 1245c04eebde Makefile --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Mon Feb 22 17:07:53 2016 -0500 @@ -0,0 +1,23 @@ +# USAGE: make [install|clean] + +# -------- VARIABLE -------- + +OBJ=xcms_summary.tgz +DEP=abims_xcms_summary.xml xcms_summary.r tool_dependencies.xml repository_dependencies.xml test-data + + +# ------------------------ + +all: $(OBJ) + +$(OBJ): $(DEP) + tar --exclude=".svn" -zchf $@ $^ + +# ------------------------ + +install: $(OBJ) + mv *.tgz ~ + +clean: + rm *.tgz + diff -r 89a8b5ff3e44 -r 1245c04eebde README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Feb 22 17:07:53 2016 -0500 @@ -0,0 +1,8 @@ + +Changelog/News +-------------- + +**Version 1.0.0 - 10/02/2016** + +- NEW: Create a summary of XCMS analysis + diff -r 89a8b5ff3e44 -r 1245c04eebde planemo.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo.sh Mon Feb 22 17:07:53 2016 -0500 @@ -0,0 +1,1 @@ +planemo shed_init -f --name=xcms_summary --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - HTML Summary for XCMS analysis" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nThis tool create a HTML summary of XCMS analysis" --category="Metabolomics" diff -r 89a8b5ff3e44 -r 1245c04eebde xcms_summary.r --- a/xcms_summary.r Fri Feb 19 11:51:18 2016 -0500 +++ b/xcms_summary.r Mon Feb 22 17:07:53 2016 -0500 @@ -42,7 +42,7 @@ if (!exists("xset") & exists("xa")) xset=xa@xcmsSet # retrocompatability -if (!exists("sampleNamesList")) sampleNamesList=list("sampleNamesMakeNames"=make.names(sampnames(xset))) +if (!exists("sampleNamesList")) sampleNamesList=List("sampleNamesMakeNames"=make.names(sampnames(xset))) if (!exists("xset")) stop("You need at least a xset or a xa object.") @@ -77,7 +77,7 @@ writehtml("
sample | ") sampleNameHtml = paste("",sampnames(xset)," | ") } else { @@ -89,13 +89,13 @@ md5sumHeaderHtml = "" md5sumHtml = "" md5sumLegend="" - } else if (is.null(md5sumList$removalBadCharacters)) { + } else if (!is.null(md5sumList$removalBadCharacters)) { md5sumHeaderHtml = paste("md5sum* | ") md5sumHtml = paste("",md5sumList$origin," | ") md5sumLegend = "md5sum* | md5sum** after bad characters removal | ") - md5sumHtml = paste("",md5sumList$origin," | ",md5sumList$removalBadCharacters," | ") + md5sumHtml = paste("",md5sumList$origin," | ",md5sumList$origin," | ") md5sumLegend = "
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