Mercurial > repos > lecorguille > xcms_group
changeset 3:98e33cdf0eb1 draft
planemo upload
| author | lecorguille |
|---|---|
| date | Mon, 22 Feb 2016 16:31:48 -0500 |
| parents | ed149026836e |
| children | 2db1d1d0f131 |
| files | Makefile README.rst abims_xcms_group.xml planemo.sh test-data/log.txt test-data/xset.group.RData tool_dependencies.xml |
| diffstat | 7 files changed, 148 insertions(+), 16 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Makefile Mon Feb 22 16:31:48 2016 -0500 @@ -0,0 +1,23 @@ +# USAGE: make [install|clean] + +# -------- VARIABLE -------- + +OBJ=xcms_group.tgz +DEP=abims_xcms_group.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 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Feb 22 16:31:48 2016 -0500 @@ -0,0 +1,19 @@ + +Changelog/News +-------------- + +**Version 2.0.4 - 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_group.xml Tue Nov 24 06:23:44 2015 -0500 +++ b/abims_xcms_group.xml Mon Feb 22 16:31:48 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_group" name="xcms.group" version="2.0.2"> +<tool id="abims_xcms_group" name="xcms.group" version="2.0.4"> <description>Group peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.</description> @@ -6,16 +6,22 @@ <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> + <command><![CDATA[ xcms.r - xfunction group image $image method $methods.method sleep 0.001 + xfunction group + image $image + + xsetRdataOutput $xsetRData + rplotspdf $rplotsPdf + + method $methods.method sleep 0.001 #if $methods.method == "density": ## minsamp $methods.minsamp minfrac $methods.minfrac @@ -35,12 +41,13 @@ rtCheck $methods.rtCheck kNN $methods.kNN #end if - && ( - mv group.RData $xsetRData; - mv Rplots.pdf $rplotsPdf - ); - cat xset.log - </command> + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" + + ]]></command> <inputs> <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> @@ -96,6 +103,7 @@ <outputs> <data name="xsetRData" format="rdata.xcms.group" label="${image.name[:-6]}.group.RData"/> <data name="rplotsPdf" format="pdf" label="${image.name[:-6]}.group.Rplots.pdf"/> + <data name="log" format="txt" label="xset.log.txt" hidden="true" /> </outputs> <tests> @@ -107,13 +115,23 @@ <param name="methods.mzwid" value="0.01"/> <param name="methods.density_options.option" value="show"/> <param name="methods.density_options.max" value="50"/> - <output name="xsetRData" file="xset.group.RData" /> - <output name="rplotsPdf" file="xset.group.Rplots.pdf" /> + <!--<output name="xsetRData" file="xset.group.RData" />--> + <!--<output name="rplotsPdf" file="xset.group.Rplots.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: 6642" /> + <has_text text="Sample classes: bio, blank" /> + </assert_contents> + </output> </test> </tests> - <help> + <help><![CDATA[ .. class:: infomark @@ -254,8 +272,28 @@ :width: 700 +--------------------------------------------------- - </help> +Changelog/News +-------------- + +**Version 2.0.4 - 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. + + + ]]></help> <citations>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/planemo.sh Mon Feb 22 16:31:48 2016 -0500 @@ -0,0 +1,1 @@ +planemo shed_init -f --name=xcms_group --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Group peaks from different samples together" --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\nGroup peaks together across samples using overlapping m/z bins and calculation of smoothed peak distributions in chromatographic time.\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics"
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log.txt Mon Feb 22 16:31:48 2016 -0500 @@ -0,0 +1,51 @@ + 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 group +image test-data/xset.RData +xsetRdataOutput test-data/xset.group.RData +rplotspdf xset.group.Rplots.pdf +method density +sleep 0.001 +minfrac 0.5 +bw 30 +mzwid 0.25 + + + INFILE PROCESSING INFO + + + ARGUMENTS PROCESSING INFO + + + MAIN PROCESSING INFO +112 175 237 300 362 425 487 550 612 675 737 800 862 925 987 +null device + 1 + + + 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: 6642 +Sample classes: bio, blank + +Profile settings: method = bin + step = 0.01 + +Memory usage: 15 MB + + + DONE
--- a/tool_dependencies.xml Tue Nov 24 06:23:44 2015 -0500 +++ b/tool_dependencies.xml Mon Feb 22 16:31:48 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>