Mercurial > repos > galaxyp > openms_mapalignerposeclustering
changeset 2:304c13ce9577 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
| author | galaxyp |
|---|---|
| date | Mon, 12 Feb 2018 12:57:02 -0500 |
| parents | 40ca4302e603 |
| children | 7f1786e1c462 |
| files | MapAlignerPoseClustering.xml SKIP_TOOLS_FILE.txt macros.xml readme.md tools_blacklist.txt |
| diffstat | 5 files changed, 51 insertions(+), 27 deletions(-) [+] |
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--- a/MapAlignerPoseClustering.xml Mon Feb 12 10:28:56 2018 -0500 +++ b/MapAlignerPoseClustering.xml Mon Feb 12 12:57:02 2018 -0500 @@ -1,9 +1,13 @@ -<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.2.0"> +<?xml version='1.0' encoding='UTF-8'?> +<!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> +<!--Proposed Tool Section: [Map Alignment]--> +<tool id="MapAlignerPoseClustering" name="MapAlignerPoseClustering" version="2.3.0"> <description>Corrects retention time distortions between maps using a pose clustering approach.</description> <macros> <token name="@EXECUTABLE@">MapAlignerPoseClustering</token> <import>macros.xml</import> </macros> + <expand macro="references"/> <expand macro="stdio"/> <expand macro="requirements"/> <command><![CDATA[ @@ -26,8 +30,6 @@ ./results_trafoxml/${infile.element_identifier}.trafoxml #end for --threads "\${GALAXY_SLOTS:-1}" - #if $param_reference_file: -reference:file $param_reference_file #end if @@ -73,7 +75,9 @@ #end if #end if #if $adv_opts.adv_opts_selector=='advanced': - + #if $adv_opts.param_force: + -force +#end if #if $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction: -algorithm:superimposer:rt_pair_distance_fraction $adv_opts.param_algorithm_superimposer_rt_pair_distance_fraction #end if @@ -83,8 +87,13 @@ #if $adv_opts.param_algorithm_superimposer_max_scaling: -algorithm:superimposer:max_scaling $adv_opts.param_algorithm_superimposer_max_scaling #end if - -#if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent: + #if $adv_opts.param_algorithm_superimposer_dump_buckets: + -algorithm:superimposer:dump_buckets "$adv_opts.param_algorithm_superimposer_dump_buckets" +#end if + #if $adv_opts.param_algorithm_superimposer_dump_pairs: + -algorithm:superimposer:dump_pairs "$adv_opts.param_algorithm_superimposer_dump_pairs" +#end if + #if $adv_opts.param_algorithm_pairfinder_distance_RT_exponent: -algorithm:pairfinder:distance_RT:exponent $adv_opts.param_algorithm_pairfinder_distance_RT_exponent #end if #if $adv_opts.param_algorithm_pairfinder_distance_RT_weight: @@ -111,7 +120,6 @@ #end if #end if #end if - ]]> </command> <inputs> @@ -133,9 +141,26 @@ <option value="ppm">ppm</option> </param> <expand macro="advanced_options"> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> <param name="param_algorithm_superimposer_rt_pair_distance_fraction" type="float" min="0.0" max="1.0" optional="True" value="0.1" label="Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min)" help="(-rt_pair_distance_fraction) "/> <param name="param_algorithm_superimposer_max_shift" type="float" min="0.0" optional="True" value="1000.0" label="Maximal shift which is considered during histogramming (in seconds)" help="(-max_shift) This applies for both directions"/> <param name="param_algorithm_superimposer_max_scaling" type="float" min="1.0" optional="True" value="2.0" label="Maximal scaling which is considered during histogramming" help="(-max_scaling) The minimal scaling is the reciprocal of this"/> + <param name="param_algorithm_superimposer_dump_buckets" type="text" size="30" label="[DEBUG] If non-empty, base filename where hash table buckets will be dumped to" help="(-dump_buckets) A serial number for each invocation will be appended automatically"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <param name="param_algorithm_superimposer_dump_pairs" type="text" size="30" label="[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!)" help="(-dump_pairs) A serial number for each invocation will be appended automatically"> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> <param name="param_algorithm_pairfinder_distance_RT_exponent" type="float" min="0.0" optional="True" value="1.0" label="Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> <param name="param_algorithm_pairfinder_distance_RT_weight" type="float" min="0.0" optional="True" value="1.0" label="Final RT distances are weighted by this facto" help="(-weight) "/> <param name="param_algorithm_pairfinder_distance_MZ_exponent" type="float" min="0.0" optional="True" value="2.0" label="Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> @@ -159,6 +184,5 @@ </outputs> <help>Corrects retention time distortions between maps using a pose clustering approach. - For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_MapAlignerPoseClustering.html</help> </tool>
--- a/SKIP_TOOLS_FILE.txt Mon Feb 12 10:28:56 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -OMSSAAdapter -MyriMatchAdapter -PepNovoAdapter -SeedListGenerator -SpecLibSearcher -MapAlignerIdentification -MapAlignerPoseClustering -MapAlignerSpectrum -MapAlignerRTTransformer
--- a/macros.xml Mon Feb 12 10:28:56 2018 -0500 +++ b/macros.xml Mon Feb 12 12:57:02 2018 -0500 @@ -2,10 +2,10 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.2">openms</requirement> + <requirement type="package" version="2.3">openms</requirement> <requirement type="package" version="15.12.15.2">xtandem</requirement> <requirement type="package" version="1.0">fido</requirement> - <requirement type="package" version="2016.10.26">msgf_plus</requirement> + <requirement type="package" version="2017.07.21">msgf_plus</requirement> <yield/> </requirements> </xml>
--- a/readme.md Mon Feb 12 10:28:56 2018 -0500 +++ b/readme.md Mon Feb 12 12:57:02 2018 -0500 @@ -53,29 +53,29 @@ * clone or install CTD2Galaxy ```bash - git clone https://github.com/WorkflowConversion/CTD2Galaxy.git + git clone https://github.com/WorkflowConversion/CTDConverter.git ``` - * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. + * If you have CTDopts and CTDConverter installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. You might have to install `libxslt` and `lxml` to run it. Further information can be found on the CTDConverter page. ```bash - python generator.py \ + python convert.py galaxy \ -i /PATH/TO/YOUR/CTD/*.ctd \ -o ./PATH/TO/YOUR/WRAPPERS/ -t tool.conf \ -d datatypes_conf.xml -g openms \ -b version log debug test no_progress threads \ in_type executable myrimatch_executable \ fido_executable fidocp_executable \ - omssa_executable pepnovo_executable \ + omssa_executable pepnovo_e xecutable \ xtandem_executable param_model_directory \ java_executable java_memory java_permgen \ r_executable rt_concat_trafo_out param_id_pool \ -f /PATH/TO/filetypes.txt -m /PATH/TO/macros.xml \ - -s PATH/TO/SKIP_TOOLS_FILES.txt + -s PATH/TO/tools_blacklist.txt ``` - * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. For example: + * As last step you need to change manually the binary names of all external binaries you want to use in OpenMS. Some of these tools might already be deprecated and the files might not exist: ``` sed -i '13 a\-fido_executable Fido' wrappers/FidoAdapter.xml @@ -171,8 +171,8 @@ ``` - * These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in - by the automatic conversion step and are therefore in `SKIP_TOOLS_FILES.txt`: + * `This section might not be up to date. It might be worth trying if these tools will run now.` These tools have multiple outputs (number of inputs = number of outputs) which is not yet supported in + by the automatic conversion step and are therefore in `tools_blacklist.txt`: * SeedListGenerator * SpecLibSearcher * MapAlignerIdentification