Mercurial > repos > tomnl > frag4feature
changeset 5:2365c3b350fa draft
planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty
| author | tomnl |
|---|---|
| date | Fri, 30 Mar 2018 10:07:11 -0400 |
| parents | db98e5d3595a |
| children | e94ce372d03d |
| files | frag4feature.R frag4feature.xml macros.xml |
| diffstat | 3 files changed, 10 insertions(+), 6 deletions(-) [+] |
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--- a/frag4feature.R Tue Mar 27 12:29:51 2018 -0400 +++ b/frag4feature.R Fri Mar 30 10:07:11 2018 -0400 @@ -19,13 +19,15 @@ nsave <- names(pa@fileList) old_filenames <- basename(pa@fileList) + pa@fileList <- filepaths[match(names(pa@fileList), galaxy_names)] names(pa@fileList) <- nsave pa@puritydf$filename <- basename(pa@fileList[match(pa@puritydf$filename, old_filenames)]) pa@grped_df$filename <- basename(pa@fileList[match(pa@grped_df$filename, old_filenames)]) } - + print(pa@fileList) + print(xset@filepaths) if(!all(basename(pa@fileList)==basename(xset@filepaths))){ if(!all(names(pa@fileList)==basename(xset@filepaths))){
--- a/frag4feature.xml Tue Mar 27 12:29:51 2018 -0400 +++ b/frag4feature.xml Fri Mar 30 10:07:11 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="frag4feature" name="frag4feature" version="0.0.15"> +<tool id="frag4feature" name="frag4feature" version="0.0.17"> <macros> <import>macros.xml</import> </macros> @@ -52,7 +52,7 @@ <inputs> <param type="data" name="xset" label="xcmsSet object" - help="xcmsSet object saved as 'xset' in an RData file" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/> + help="grouped xcmsSet object saved as 'xset' in an RData file" format="rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata.camera.quick,rdata.camera.positive,rdata.camera.negative,rdata"/> <param type="data" name="pa" label="purityA object" format="rdata" help="purityA object saved as 'pa' in a RData file (output from assess_purity_msms)"/> @@ -111,7 +111,9 @@ Description ----------- -Tool to link XCMS features to fragmentation spectra and create an SQLite database of all the data and connections. +Tool to link XCMS features to fragmentation spectra and create an SQLite database of all the data and connections. + +Please note that the xcmsSet object needs to have been grouped. The data inputs are: @@ -119,7 +121,7 @@ * A xcmsSet grouped object (generated from xcms_group) saved in an rdata file * [optional] a dataset collection of the mzML files to resubmit -See Bioconductor documentation for more details, function msPurity::dimsPredictPurity() +See Bioconductor documentation for more details, function msPurity::frag4feature() ----------- Outputs
--- a/macros.xml Tue Mar 27 12:29:51 2018 -0400 +++ b/macros.xml Fri Mar 30 10:07:11 2018 -0400 @@ -2,7 +2,7 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.5.2" >bioconductor-mspurity</requirement> + <requirement type="package" version="1.5.4" >bioconductor-mspurity</requirement> <requirement type="package" version="1.4.4" >r-optparse</requirement> <yield /> </requirements>