Mercurial > repos > galaxyp > openms_psmfeatureextractor
diff PSMFeatureExtractor.xml @ 0:16a3498124d1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author | galaxyp |
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date | Mon, 12 Feb 2018 13:40:23 -0500 |
parents | |
children | 54ff34feb43d |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PSMFeatureExtractor.xml Mon Feb 12 13:40:23 2018 -0500 @@ -0,0 +1,89 @@ +<?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: [Utilities]--> +<tool id="PSMFeatureExtractor" name="PSMFeatureExtractor" version="2.3.0"> + <description>Computes extra features for each input PSM.</description> + <macros> + <token name="@EXECUTABLE@">PSMFeatureExtractor</token> + <import>macros.xml</import> + </macros> + <expand macro="references"/> + <expand macro="stdio"/> + <expand macro="requirements"/> + <command>PSMFeatureExtractor + +-in + #for token in $param_in: + $token + #end for +#if $param_out: + -out $param_out +#end if + +#if $rep_param_extra: +-extra + #for token in $rep_param_extra: + #if " " in str(token): + "$token.param_extra" + #else + $token.param_extra + #end if + #end for +#end if +#if $param_multiple_search_engines: + -multiple_search_engines +#end if +#if $adv_opts.adv_opts_selector=='advanced': + #if $adv_opts.param_skip_db_check: + -skip_db_check +#end if + #if $adv_opts.param_concat: + -concat +#end if + #if $adv_opts.param_impute: + -impute +#end if + #if $adv_opts.param_limit_imputation: + -limit_imputation +#end if + #if $adv_opts.param_force: + -force +#end if +#end if +</command> + <inputs> + <param name="param_in" type="data" format="mzid,idxml" multiple="true" optional="False" size="30" label="Input file(s)" help="(-in) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + <repeat name="rep_param_extra" min="0" title="param_extra"> + <param name="param_extra" type="text" size="30" label="List of the MetaData parameters to be included in a feature set for precolato" help="(-extra) "> + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + <remove value="""/> + </valid> + </sanitizer> + </param> + </repeat> + <param name="param_multiple_search_engines" display="radio" type="boolean" truevalue="-multiple_search_engines" falsevalue="" checked="false" optional="True" label="Combine PSMs from different search engines by merging on scan level" help="(-multiple_search_engines) "/> + <expand macro="advanced_options"> + <param name="param_skip_db_check" display="radio" type="boolean" truevalue="-skip_db_check" falsevalue="" checked="false" optional="True" label="Manual override to skip the check if same settings for multiple search engines were applied" help="(-skip_db_check) Only valid together with -multiple_search_engines flag"/> + <param name="param_concat" display="radio" type="boolean" truevalue="-concat" falsevalue="" checked="false" optional="True" label="Naive merging of PSMs from different search engines: concatenate multiple search results instead of merging on scan level" help="(-concat) Only valid together with -multiple_search_engines flag"/> + <param name="param_impute" display="radio" type="boolean" truevalue="-impute" falsevalue="" checked="false" optional="True" label="Will instead of discarding all PSM not unanimously detected by all SE, impute missing values by their respective scores min/max observed" help="(-impute) Only valid together with -multiple_search_engines flag"/> + <param name="param_limit_imputation" display="radio" type="boolean" truevalue="-limit_imputation" falsevalue="" checked="false" optional="True" label="Will impute missing scores with the worst numerical limit (instead of min/max observed) of the respective score" help="(-limit_imputation) Only valid together with -multiple_search_engines flag"/> + <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> + </expand> + </inputs> + <outputs> + <data name="param_out" metadata_source="param_in" format="input"/> + </outputs> + <help>Computes extra features for each input PSM. + + +For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_PSMFeatureExtractor.html</help> +</tool>