Mercurial > repos > lecorguille > xcms_xcmsset
changeset 1:2f5b78be1dd6 draft
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--- 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 -
--- 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 - && (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>
--- 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"
--- /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 @@ +10 + +dir +157 +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_xcmsset/static +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo + + + +2015-08-03T13:28:59.062143Z +155 +lecorguille + + + + + + + + + + + + + + +87d02074-be8c-4456-a071-04b64888326c + +images +dir +
--- /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 @@ +10 + +dir +157 +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_xcmsset/static/images +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo + + + +2015-08-03T13:28:59.062143Z +155 +lecorguille + + + + + + + + + + + + + + +87d02074-be8c-4456-a071-04b64888326c + +xcms_tics.png +file + + + + +2015-08-03T08:04:43.000000Z +caa449c237f7fe3681d313870ff165b9 +2015-08-03T13:28:59.062143Z +155 +lecorguille +has-props + + + + + + + + + + + + + + + + + + + + +66110 + +XCMS_Galaxy_workflow.png +file + + + + +2015-08-03T08:04:43.000000Z +892d1ad7a6f70a22b601de3971c13b5b +2015-08-03T13:28:59.062143Z +155 +lecorguille +has-props + + + + + + + + + + + + + + + + + + + + +60834 +
--- /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 @@ +K 14 +svn:executable +V 1 +* +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /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 @@ +K 14 +svn:executable +V 1 +* +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /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 @@ +10 + +dir +157 +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_xcmsset/test-data +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo + + + +2015-08-03T13:28:59.062143Z +155 +lecorguille + + + + + + + + + + + + + + +87d02074-be8c-4456-a071-04b64888326c + +xset.log.txt +file + + + + +2015-08-03T12:51:24.000000Z +2381f7db69ed8fd6359f34f9e5a93fdf +2015-08-03T13:28:59.062143Z +155 +lecorguille + + + + + + + + + + + + + + + + + + + + + +1182 + +xset.TICs_raw.pdf +file + + + + +2015-08-03T12:50:47.000000Z +5aeb9e5477d43db6016c73757dde0ecd +2015-08-03T13:28:59.062143Z +155 +lecorguille +has-props + + + + + + + + + + + + + + + + + + + + +101839 + +sacuri.zip +file + + + + +2015-08-03T12:44:17.000000Z +3d83830cc23dba9bfcbcaa1cf40b6fe1 +2015-08-03T13:28:59.062143Z +155 +lecorguille +has-props + + + + + + + + + + + + + + + + + + + + +50550100 + +xset.BPCs_raw.pdf +file + + + + +2015-08-03T12:51:09.000000Z +bed51a67a170a3ae7b2e592564e9aba7 +2015-08-03T13:28:59.062143Z +155 +lecorguille + + + + + + + + + + + + + + + + + + + + + +99916 + +xset.RData +file + + + + +2015-08-03T12:50:06.000000Z +04afedd30804e678bfc82e2161db85a2 +2015-08-03T13:28:59.062143Z +155 +lecorguille +has-props + + + + + + + + + + + + + + + + + + + + +7586577 + +sampleMetadata.tsv +file + + + + +2015-08-03T12:51:01.000000Z +11b743a21f5b1bd1f87b09858b1d2bcf +2015-08-03T13:28:59.062143Z +155 +lecorguille + + + + + + + + + + + + + + + + + + + + + +242 +
--- /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 @@ +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /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 @@ +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /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 @@ +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /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
--- /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
--- /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
--- 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
--- 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" />