Mercurial > repos > galaxyp > openms_featurelinkerunlabeled
diff FeatureLinkerUnlabeled.xml @ 11:6b88274392ce draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
| author | galaxyp |
|---|---|
| date | Wed, 09 Sep 2020 12:49:46 +0000 |
| parents | bc21e5dd5ff0 |
| children | a6e006df7659 |
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--- a/FeatureLinkerUnlabeled.xml Fri May 17 09:53:15 2019 -0400 +++ b/FeatureLinkerUnlabeled.xml Wed Sep 09 12:49:46 2020 +0000 @@ -1,124 +1,110 @@ <?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="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="2.3.0"> +<tool id="FeatureLinkerUnlabeled" name="FeatureLinkerUnlabeled" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Groups corresponding features from multiple maps.</description> <macros> <token name="@EXECUTABLE@">FeatureLinkerUnlabeled</token> <import>macros.xml</import> + <import>macros_autotest.xml</import> + <import>macros_test.xml</import> </macros> - <expand macro="references"/> + <expand macro="requirements"/> <expand macro="stdio"/> - <expand macro="requirements"/> - <command detect_errors="aggressive"><![CDATA[FeatureLinkerUnlabeled + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re --in - #for token in $param_in: - $token - #end for -#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_second_nearest_gap: - -algorithm:second_nearest_gap $param_algorithm_second_nearest_gap -#end if -#if $param_algorithm_use_identifications: - -algorithm:use_identifications +## Preprocessing +mkdir in && +${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } +mkdir out && +#if $design: + mkdir design && + ln -s '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' && #end if -#if $param_algorithm_ignore_charge: - -algorithm:ignore_charge -#end if -#if $param_algorithm_distance_RT_max_difference: - -algorithm:distance_RT:max_difference $param_algorithm_distance_RT_max_difference -#end if -#if $param_algorithm_distance_MZ_max_difference: - -algorithm:distance_MZ:max_difference $param_algorithm_distance_MZ_max_difference -#end if -#if $param_algorithm_distance_MZ_unit: - -algorithm:distance_MZ:unit - #if " " in str($param_algorithm_distance_MZ_unit): - "$param_algorithm_distance_MZ_unit" - #else - $param_algorithm_distance_MZ_unit - #end if -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if - #if $adv_opts.param_algorithm_distance_RT_exponent: - -algorithm:distance_RT:exponent $adv_opts.param_algorithm_distance_RT_exponent -#end if - #if $adv_opts.param_algorithm_distance_RT_weight: - -algorithm:distance_RT:weight $adv_opts.param_algorithm_distance_RT_weight + +## Main program call + +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} +-out +'out/output.${gxy2omsext("consensusxml")}' +#if $design: + -design + 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' #end if - #if $adv_opts.param_algorithm_distance_MZ_exponent: - -algorithm:distance_MZ:exponent $adv_opts.param_algorithm_distance_MZ_exponent -#end if - #if $adv_opts.param_algorithm_distance_MZ_weight: - -algorithm:distance_MZ:weight $adv_opts.param_algorithm_distance_MZ_weight -#end if - #if $adv_opts.param_algorithm_distance_intensity_exponent: - -algorithm:distance_intensity:exponent $adv_opts.param_algorithm_distance_intensity_exponent -#end if - #if $adv_opts.param_algorithm_distance_intensity_weight: - -algorithm:distance_intensity:weight $adv_opts.param_algorithm_distance_intensity_weight -#end if - #if $adv_opts.param_algorithm_distance_intensity_log_transform: - -algorithm:distance_intensity:log_transform - #if " " in str($adv_opts.param_algorithm_distance_intensity_log_transform): - "$adv_opts.param_algorithm_distance_intensity_log_transform" - #else - $adv_opts.param_algorithm_distance_intensity_log_transform - #end if -#end if -#end if -]]></command> + +## Postprocessing +&& mv 'out/output.${gxy2omsext("consensusxml")}' '$out' +#if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS + && mv '@EXECUTABLE@.ctd' '$ctd_out' +#end if]]></command> + <configfiles> + <inputs name="args_json" data_style="paths"/> + <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> + </configfiles> <inputs> - <param name="param_in" type="data" format="featurexml,consensusxml" multiple="true" optional="False" size="30" label="input files separated by blanks" help="(-in) "> - <sanitizer> - <valid initial="string.printable"> - <remove value="'"/> - <remove value="""/> - </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_second_nearest_gap" type="float" min="1.0" optional="True" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help="(-second_nearest_gap) "/> - <param name="param_algorithm_use_identifications" display="radio" type="boolean" truevalue="-algorithm:use_identifications" falsevalue="" checked="false" optional="True" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help="(-use_identifications) "/> - <param name="param_algorithm_ignore_charge" display="radio" type="boolean" truevalue="-algorithm:ignore_charge" falsevalue="" checked="false" optional="True" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help="(-ignore_charge) "/> - <param name="param_algorithm_distance_RT_max_difference" type="float" min="0.0" optional="True" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help="(-max_difference) "/> - <param name="param_algorithm_distance_MZ_max_difference" type="float" min="0.0" optional="True" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help="(-max_difference) "/> - <param name="param_algorithm_distance_MZ_unit" display="radio" type="select" optional="False" value="Da" label="Unit of the 'max_difference' paramete" help="(-unit) "> - <option value="Da" selected="true">Da</option> - <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_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) "/> - <param name="param_algorithm_distance_MZ_weight" type="float" min="0.0" optional="True" value="1.0" label="Final m/z distances are weighted by this facto" help="(-weight) "/> - <param name="param_algorithm_distance_intensity_exponent" type="float" min="0.0" optional="True" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help="(-exponent) "/> - <param name="param_algorithm_distance_intensity_weight" type="float" min="0.0" optional="True" value="0.0" label="Final intensity distances are weighted by this facto" help="(-weight) "/> - <param name="param_algorithm_distance_intensity_log_transform" display="radio" type="select" optional="False" value="disabled" label="Log-transform intensities?" help="(-log_transform) If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))"> - <option value="enabled">enabled</option> - <option value="disabled" selected="true">disabled</option> + <param name="in" argument="-in" type="data" format="consensusxml,featurexml" multiple="true" optional="false" label="input files separated by blanks" help=" select consensusxml,featurexml data sets(s)"/> + <param name="design" argument="-design" type="data" format="tabular" optional="true" label="input file containing the experimental design" help=" select tabular data sets(s)"/> + <param name="keep_subelements" argument="-keep_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For consensusXML input only: If set, the sub-features of the inputs are transferred to the output" help=""/> + <section name="algorithm" title="Algorithm parameters section" help="" expanded="false"> + <param name="second_nearest_gap" argument="-algorithm:second_nearest_gap" type="float" optional="true" min="1.0" value="2.0" label="Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself" help=""/> + <param name="use_identifications" argument="-algorithm:use_identifications" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered)" help=""/> + <param name="ignore_charge" argument="-algorithm:ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state" help=""/> + <param name="ignore_adduct" argument="-algorithm:ignore_adduct" type="boolean" truevalue="true" falsevalue="false" checked="true" label="true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts" help=""/> + <section name="distance_RT" title="Distance component based on RT differences" help="" expanded="false"> + <param name="max_difference" argument="-algorithm:distance_RT:max_difference" type="float" optional="true" min="0.0" value="100.0" label="Never pair features with a larger RT distance (in seconds)" help=""/> + <param name="exponent" argument="-algorithm:distance_RT:exponent" type="float" optional="true" min="0.0" 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=""/> + <param name="weight" argument="-algorithm:distance_RT:weight" type="float" optional="true" min="0.0" value="1.0" label="Final RT distances are weighted by this facto" help=""/> + </section> + <section name="distance_MZ" title="Distance component based on m/z differences" help="" expanded="false"> + <param name="max_difference" argument="-algorithm:distance_MZ:max_difference" type="float" optional="true" min="0.0" value="0.3" label="Never pair features with larger m/z distance (unit defined by 'unit')" help=""/> + <param name="unit" argument="-algorithm:distance_MZ:unit" display="radio" type="select" optional="false" label="Unit of the 'max_difference' paramete" help=""> + <option value="Da" selected="true">Da</option> + <option value="ppm">ppm</option> + <expand macro="list_string_san"/> + </param> + <param name="exponent" argument="-algorithm:distance_MZ:exponent" type="float" optional="true" min="0.0" 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=""/> + <param name="weight" argument="-algorithm:distance_MZ:weight" type="float" optional="true" min="0.0" value="1.0" label="Final m/z distances are weighted by this facto" help=""/> + </section> + <section name="distance_intensity" title="Distance component based on differences in relative intensity (usually relative to highest peak in the whole data set)" help="" expanded="false"> + <param name="exponent" argument="-algorithm:distance_intensity:exponent" type="float" optional="true" min="0.0" value="1.0" label="Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)" help=""/> + <param name="weight" argument="-algorithm:distance_intensity:weight" type="float" optional="true" min="0.0" value="0.0" label="Final intensity distances are weighted by this facto" help=""/> + <param name="log_transform" argument="-algorithm:distance_intensity:log_transform" display="radio" type="select" optional="false" label="Log-transform intensities" help="If disabled, d = |int_f2 - int_f1| / int_max. If enabled, d = |log(int_f2 + 1) - log(int_f1 + 1)| / log(int_max + 1))"> + <option value="enabled">enabled</option> + <option value="disabled" selected="true">disabled</option> + <expand macro="list_string_san"/> + </param> + </section> + </section> + <expand macro="adv_opts_macro"> + <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> + <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> + <expand macro="list_string_san"/> </param> </expand> + <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> + <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> + </param> </inputs> <outputs> - <data name="param_out" format="consensusxml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Groups corresponding features from multiple maps. + <tests> + <expand macro="autotest_FeatureLinkerUnlabeled"/> + <expand macro="manutest_FeatureLinkerUnlabeled"/> + </tests> + <help><![CDATA[Groups corresponding features from multiple maps. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_FeatureLinkerUnlabeled.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_FeatureLinkerUnlabeled.html]]></help> + <expand macro="references"/> </tool>