Mercurial > repos > galaxyp > openms_featurelinkerunlabeledkd
changeset 4:17aa0e144300 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
| author | galaxyp |
|---|---|
| date | Mon, 12 Feb 2018 13:02:25 -0500 |
| parents | b97fe2b25b08 |
| children | 0fb771921feb |
| files | FeatureLinkerUnlabeledKD.xml SKIP_TOOLS_FILE.txt macros.xml readme.md tools_blacklist.txt |
| diffstat | 5 files changed, 59 insertions(+), 47 deletions(-) [+] |
line wrap: on
line diff
--- a/FeatureLinkerUnlabeledKD.xml Thu Jan 11 18:02:12 2018 -0500 +++ b/FeatureLinkerUnlabeledKD.xml Mon Feb 12 13:02:25 2018 -0500 @@ -1,7 +1,7 @@ <?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 CTD2Galaxy.--> +<!--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="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="2.2.0"> +<tool id="FeatureLinkerUnlabeledKD" name="FeatureLinkerUnlabeledKD" version="2.3.0"> <description>Groups corresponding features from multiple maps.</description> <macros> <token name="@EXECUTABLE@">FeatureLinkerUnlabeledKD</token> @@ -19,15 +19,12 @@ #if $param_out: -out $param_out #end if +#if $param_design: + -design $param_design +#end if #if $param_keep_subelements: -keep_subelements #end if -#if $param_algorithm_rt_tol: - -algorithm:rt_tol $param_algorithm_rt_tol -#end if -#if $param_algorithm_mz_tol: - -algorithm:mz_tol $param_algorithm_mz_tol -#end if #if $param_algorithm_mz_unit: -algorithm:mz_unit #if " " in str($param_algorithm_mz_unit): @@ -36,29 +33,41 @@ $param_algorithm_mz_unit #end if #end if -#if $param_algorithm_warp: - -algorithm:warp - #if " " in str($param_algorithm_warp): - "$param_algorithm_warp" +#if $param_algorithm_nr_partitions: + -algorithm:nr_partitions $param_algorithm_nr_partitions +#end if +#if $param_algorithm_warp_enabled: + -algorithm:warp:enabled + #if " " in str($param_algorithm_warp_enabled): + "$param_algorithm_warp_enabled" #else - $param_algorithm_warp + $param_algorithm_warp_enabled #end if #end if -#if $param_algorithm_nr_partitions: - -algorithm:nr_partitions $param_algorithm_nr_partitions +#if $param_algorithm_warp_rt_tol: + -algorithm:warp:rt_tol $param_algorithm_warp_rt_tol +#end if +#if $param_algorithm_warp_mz_tol: + -algorithm:warp:mz_tol $param_algorithm_warp_mz_tol +#end if +#if $param_algorithm_link_rt_tol: + -algorithm:link:rt_tol $param_algorithm_link_rt_tol +#end if +#if $param_algorithm_link_mz_tol: + -algorithm:link:mz_tol $param_algorithm_link_mz_tol #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: -force #end if - #if $adv_opts.param_algorithm_max_pairwise_log_fc: - -algorithm:max_pairwise_log_fc $adv_opts.param_algorithm_max_pairwise_log_fc + #if $adv_opts.param_algorithm_warp_max_pairwise_log_fc: + -algorithm:warp:max_pairwise_log_fc $adv_opts.param_algorithm_warp_max_pairwise_log_fc #end if - #if $adv_opts.param_algorithm_min_rel_cc_size: - -algorithm:min_rel_cc_size $adv_opts.param_algorithm_min_rel_cc_size + #if $adv_opts.param_algorithm_warp_min_rel_cc_size: + -algorithm:warp:min_rel_cc_size $adv_opts.param_algorithm_warp_min_rel_cc_size #end if - #if $adv_opts.param_algorithm_max_nr_conflicts: - -algorithm:max_nr_conflicts $adv_opts.param_algorithm_max_nr_conflicts + #if $adv_opts.param_algorithm_warp_max_nr_conflicts: + -algorithm:warp:max_nr_conflicts $adv_opts.param_algorithm_warp_max_nr_conflicts #end if #if $adv_opts.param_algorithm_distance_RT_exponent: -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent @@ -122,23 +131,26 @@ </valid> </sanitizer> </param> + <param name="param_design" type="data" format="tabular" optional="True" label="input file containing the experimental design" help="(-design) "/> <param name="param_keep_subelements" display="radio" type="boolean" truevalue="-keep_subelements" falsevalue="" checked="false" optional="True" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help="(-keep_subelements) "/> - <param name="param_algorithm_rt_tol" type="float" min="0.0" optional="True" value="60.0" label="Width of RT tolerance window (sec)" help="(-rt_tol) "/> - <param name="param_algorithm_mz_tol" type="float" min="0.0" optional="True" value="15.0" label="m/z tolerance (in ppm or Da)" help="(-mz_tol) "/> <param name="param_algorithm_mz_unit" display="radio" type="select" optional="False" value="ppm" label="Unit of m/z tolerance" help="(-mz_unit) "> <option value="ppm" selected="true">ppm</option> <option value="Da">Da</option> </param> - <param name="param_algorithm_warp" display="radio" type="select" optional="False" value="true" label="Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)" help="(-warp) "> + <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="100" label="Number of partitions in m/z space" help="(-nr_partitions) "/> + <param name="param_algorithm_warp_enabled" display="radio" type="select" optional="False" value="true" label="Whether or not to internally warp feature RTs using LOWESS transformation before linking (reported RTs in results will always be the original RTs)" help="(-enabled) "> <option value="true" selected="true">true</option> <option value="false">false</option> </param> - <param name="param_algorithm_nr_partitions" type="integer" min="1" optional="True" value="100" label="Number of partitions in m/z space" help="(-nr_partitions) "/> + <param name="param_algorithm_warp_rt_tol" type="float" min="0.0" optional="True" value="100.0" label="Width of RT tolerance window (sec)" help="(-rt_tol) "/> + <param name="param_algorithm_warp_mz_tol" type="float" min="0.0" optional="True" value="5.0" label="m/z tolerance (in ppm or Da)" help="(-mz_tol) "/> + <param name="param_algorithm_link_rt_tol" type="float" min="0.0" optional="True" value="30.0" label="Width of RT tolerance window (sec)" help="(-rt_tol) "/> + <param name="param_algorithm_link_mz_tol" type="float" min="0.0" optional="True" value="10.0" label="m/z tolerance (in ppm or Da)" help="(-mz_tol) "/> <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_max_pairwise_log_fc" type="float" value="0.5" label="Only relevant during RT alignment ('warp' set to 'true'): Maximum absolute log10 fold change between two compatible signals during compatibility graph construction" help="(-max_pairwise_log_fc) Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value < 0 disables the FC check"/> - <param name="param_algorithm_min_rel_cc_size" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Only relevant during RT alignment ('warp' set to 'true'): Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function" help="(-min_rel_cc_size) "/> - <param name="param_algorithm_max_nr_conflicts" type="integer" min="-1" optional="True" value="0" label="Only relevant during RT alignment ('warp' set to 'true'): Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help="(-max_nr_conflicts) "/> + <param name="param_algorithm_warp_max_pairwise_log_fc" type="float" value="0.5" label="Maximum absolute log10 fold change between two compatible signals during compatibility graph construction" help="(-max_pairwise_log_fc) Two signals from different maps will not be connected by an edge in the compatibility graph if absolute log fold change exceeds this limit (they might still end up in the same connected component, however). Note: this does not limit fold changes in the linking stage, only during RT alignment, where we try to find high-quality alignment anchor points. Setting this to a value < 0 disables the FC check"/> + <param name="param_algorithm_warp_min_rel_cc_size" type="float" min="0.0" max="1.0" optional="True" value="0.5" label="Only connected components containing compatible features from at least max(2, (warp_min_occur * number_of_input_maps)) input maps are considered for computing the warping function" help="(-min_rel_cc_size) "/> + <param name="param_algorithm_warp_max_nr_conflicts" type="integer" min="-1" optional="True" value="0" label="Allow up to this many conflicts (features from the same map) per connected component to be used for alignment (-1 means allow any number of conflicts)" help="(-max_nr_conflicts) "/> <param name="param_algorithm_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_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_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) "/>
--- a/SKIP_TOOLS_FILE.txt Thu Jan 11 18:02:12 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 Thu Jan 11 18:02:12 2018 -0500 +++ b/macros.xml Mon Feb 12 13:02:25 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 Thu Jan 11 18:02:12 2018 -0500 +++ b/readme.md Mon Feb 12 13:02:25 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