Mercurial > repos > lecorguille > xcms_xcmsset
changeset 26:626d3db664ef draft
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit b1ebca6e0188e0aa0645e67259d6729ce80a6bdf
| author | lecorguille |
|---|---|
| date | Wed, 22 Mar 2017 16:04:45 -0400 |
| parents | dc4d3e2b9968 |
| children | 8e46e9bd7c50 |
| files | Makefile README.rst abims_xcms_xcmsSet.xml destinations_input_type.py job_conf.xml.sample |
| diffstat | 5 files changed, 90 insertions(+), 36 deletions(-) [+] |
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--- a/Makefile Thu Mar 02 08:20:04 2017 -0500 +++ /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/README.rst Thu Mar 02 08:20:04 2017 -0500 +++ b/README.rst Wed Mar 22 16:04:45 2017 -0400 @@ -1,11 +1,33 @@ +Job Dynamic Destination Mapping +------------------------------- + +**Why** + +xcmsSet wrapper allow both individual file and zip file which can contain several samples. +Thus, it can be interesting to adjust the number of thread according to the input type. +For example: 1 thread for a single mzXML or NetCDF file and 8 threads for a zip file. + +**What** + +The [Dynamic Destination Mapping](https://galaxyproject.org/admin/config/jobs/#dynamic-destination-mapping) allow Galaxy to choose a destination at runtime based on factors such as the job inputs, user submitting the job, cluster status, etc... + +**How** + + - The file `destinations_input_type.py` (shiped with this tool) must be place in `lib/galaxy/jobs/rules/` + - The `job_conf.xml` must be inspired by the `job_conf.xml.sample` shiped with this tool + - The final destination names must match between the `job_conf.xml` and the `destinations_input_type.py` + - Restart Galaxy + Changelog/News -------------- -**Version 2.1.0 - 03/02/2017** +**Version 2.1.0 - 22/02/2017** - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group". +- BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1 + **Version 2.0.11 - 22/12/2016** - BUGFIX: propose scanrange for all methods @@ -53,4 +75,3 @@ - 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_xcmsSet.xml Thu Mar 02 08:20:04 2017 -0500 +++ b/abims_xcms_xcmsSet.xml Wed Mar 22 16:04:45 2017 -0400 @@ -48,9 +48,8 @@ ## sigma "$methods.options_m.sigma" max $methods.options_m.max snthresh $methods.options_m.snthresh - ## mzdiff $methods.options_m.mzdiff steps $methods.options_m.steps - ## sleep $methods.options_m.sleep + mzdiff $methods.options_m.mzdiff #end if #elif $methods.method == "MSW": snthr $methods.snthr @@ -109,7 +108,7 @@ </param> <when value="show"> <param name="snthresh" type="integer" value="10" label="Signal/Noise threshold" help="[snthresh] Signal to noise ratio cutoff" /> - <param name="mzdiff" type="float" value="-0.001" label="Min m/z difference" help="[mzdiff] Min m/z difference for peaks with overlapping RT " /> + <param name="mzdiff" type="float" value="-0.001" label="Minimum difference in m/z for peaks with overlapping retention times" help="[mzdiff] Can be negative to allow overlap" /> <param name="integrate" type="select" label="peak limits method" help="[integrate]" > <option value="1">peak limits based on smoothed 2nd derivative (less precise)</option> <option value="2">peak limits based on real data (more sensitive to noise)</option> @@ -124,7 +123,7 @@ <!-- matched Filter options --> <when value="matchedFilter"> - <param name="step" type="float" value="0.01" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> + <param name="step" type="float" value="0.1" label="Step size to use for profile generation" help="[step] The peak detection algorithm creates extracted ion base peak chromatograms (EIBPC) on a fixed step size" /> <param name="fwhm" type="integer" value="30" label="Full width at half maximum of matched filtration gaussian model peak" help="[fwhm] Only used to calculate the actual sigma" /> <conditional name="options_m"> <param name="option" type="select" label="Advanced options" > @@ -132,15 +131,11 @@ <option value="hide" selected="true">hide</option> </param> <when value="show"> -<!-- - <param name="sigma" type="hidden" value="fwhm/2.3548" label="sigma" help="standard deviation (fwhm/2.3548)" /> ---> + <!--<param name="sigma" type="float" value="12.739935451" label="Standard deviation (width) of matched filtration model peak" help="[sigma] By default: fwhm/2.3548" />--> <param name="max" type="integer" value="5" label="Maximum number of peaks per extracted ion chromatogram" help="[max]" /> <param name="snthresh" type="integer" value="10" label="Signal to noise ratio cutoff" help="[snthresh]" /> <param name="steps" type="integer" value="2" label="Number of steps to merge prior to filtration" help="[steps] The peak identification algorithm combines a given number of EIBPCs prior to filtration and peak detection, as defined by the steps argument" /> -<!-- - <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 " /> ---> + <param name="mzdiff" type="float" value="0.6" label="Minimum difference in m/z for peaks with overlapping Retention Times" help="[mzdiff] By default: 0.8-step*steps " /> </when> <when value="hide"> </when> @@ -562,10 +557,12 @@ Changelog/News -------------- -**Version 2.1.0 - 03/02/2017** +**Version 2.1.0 - 22/02/2017** - NEW: The W4M tools will be able now to take as input a single file. It will allow to submit in parallel several files and merge them afterward using "xcms.xcmsSet Merger" before "xcms.group". +- BUGFIX: the default value of "matchedFilter" -> "Step size to use for profile generation" which was of 0.01 have been changed to fix with the XMCS default values to 0.1 + **Version 2.0.11 - 22/12/2016** - BUGFIX: propose scanrange for all methods
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/destinations_input_type.py Wed Mar 22 16:04:45 2017 -0400 @@ -0,0 +1,23 @@ +from galaxy.jobs import JobDestination +import logging +import os + +''' +This file must be placed in lib/galaxy/jobs/rules/ +''' + +def input_type(job): + ''' + This function checks the input file format/extension and decide which destination in the job_conf.xml using + - If it's a zip file, we will launch the job in multi-thread mode (-pe thread 8) + - If it's an individual file (mzxml, mzml, mzdata or netcdf), the job will use for instance (-pe thread 1) + ''' + log = logging.getLogger(__name__) + inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] ) + inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] ) + input_extension = inp_data[ "input" ].extension + log.debug("The input extension is %s" % input_extension) + if input_extension in ["mzxml","mzml","mzdata","netcdf"]: + return 'thread1-men_free10' + else: # zip file + return 'thread4-men_free10'
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/job_conf.xml.sample Wed Mar 22 16:04:45 2017 -0400 @@ -0,0 +1,36 @@ +<?xml version="1.0"?> +<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). --> +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + <plugin id="sge" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" type="runner"/> + <plugin id="dynamic" type="runner" > + <param id="rules_module">galaxy.jobs.rules</param> + </plugin> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations default="sge_default"> + <destination id="local" runner="local"/> + <destination id="sge_default" runner="sge"> + <param id="nativeSpecification">-V -w n -q galaxy.q</param> + </destination> + + <destination id="thread1-men_free10" runner="sge"> + <param id="nativeSpecification">-V -w n -q galaxy.q -pe thread 1 -R y -l mem_free=10G </param> + </destination> + <destination id="thread4-men_free10" runner="sge"> + <param id="nativeSpecification">-V -w n -q galaxy.q -pe thread 4 -R y -l mem_free=10G </param> + </destination> + + <destination id="python_destination_input_type" runner="dynamic"> + <param id="type">python</param> + <param id="function">input_type</param> + </destination> + </destinations> + <tools> + <tool destination="python_destination_input_type" id="abims_xcms_xcmsSet" /> + <tool destination="local" id="upload1"/> + </tools> +</job_conf>