Mercurial > repos > galaxyp > openms_phosphoscoring
diff PhosphoScoring.xml @ 9:4c583fde2a28 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author | galaxyp |
---|---|
date | Wed, 09 Sep 2020 19:45:14 +0000 |
parents | 3392cf4c19bb |
children | c04ff2777ed2 |
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--- a/PhosphoScoring.xml Fri May 17 09:18:13 2019 -0400 +++ b/PhosphoScoring.xml Wed Sep 09 19:45:14 2020 +0000 @@ -1,68 +1,84 @@ <?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: [ID Processing]--> -<tool id="PhosphoScoring" name="PhosphoScoring" version="2.3.0"> +<tool id="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description> <macros> <token name="@EXECUTABLE@">PhosphoScoring</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[PhosphoScoring + <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ +@EXT_FOO@ +#import re + +## Preprocessing +mkdir in && +ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && +mkdir id && +ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' && +mkdir out && + +## Main program call -#if $param_in: - -in $param_in -#end if -#if $param_id: - -id $param_id -#end if -#if $param_out: - -out $param_out -#end if -#if $param_fragment_mass_tolerance: - -fragment_mass_tolerance $param_fragment_mass_tolerance -#end if -#if $param_fragment_mass_unit: - -fragment_mass_unit - #if " " in str($param_fragment_mass_unit): - "$param_fragment_mass_unit" - #else - $param_fragment_mass_unit - #end if -#end if -#if $param_max_peptide_length: - -max_peptide_length $param_max_peptide_length -#end if -#if $param_max_num_perm: - -max_num_perm $param_max_num_perm -#end if -#if $adv_opts.adv_opts_selector=='advanced': - #if $adv_opts.param_force: - -force -#end if -#end if -]]></command> +set -o pipefail && +@EXECUTABLE@ -write_ctd ./ && +python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && +@EXECUTABLE@ -ini @EXECUTABLE@.ctd +-in +'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' +-id +'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' +-out +'out/output.${gxy2omsext("idxml")}' + +## Postprocessing +&& mv 'out/output.${gxy2omsext("idxml")}' '$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="mzml" optional="False" label="Input file with MS/MS spectra" help="(-in) "/> - <param name="param_id" type="data" format="idxml" optional="False" label="Identification input file which contains a search against a concatenated sequence database" help="(-id) "/> - <param name="param_fragment_mass_tolerance" type="float" value="0.05" label="Fragment mass erro" help="(-fragment_mass_tolerance) "/> - <param name="param_fragment_mass_unit" display="radio" type="select" optional="False" value="Da" label="Unit of fragment mass erro" help="(-fragment_mass_unit) "> + <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/> + <param name="id" argument="-id" type="data" format="idxml" optional="false" label="Identification input file which contains a search against a concatenated sequence database" help=" select idxml data sets(s)"/> + <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/> + <param name="fragment_mass_unit" argument="-fragment_mass_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help=""> <option value="Da" selected="true">Da</option> <option value="ppm">ppm</option> + <expand macro="list_string_san"/> </param> - <param name="param_max_peptide_length" type="integer" min="1" optional="True" value="40" label="Restrict scoring to peptides with a length shorter than this value" help="(-max_peptide_length) "/> - <param name="param_max_num_perm" type="integer" min="1" optional="True" value="16384" label="Maximum number of permutations a sequence can have" help="(-max_num_perm) "/> - <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) "/> + <expand macro="adv_opts_macro"> + <param name="max_peptide_length" argument="-max_peptide_length" type="integer" optional="true" min="0" value="40" label="Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')" help=""/> + <param name="max_num_perm" argument="-max_num_perm" type="integer" optional="true" min="0" value="16384" label="Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')" help=""/> + <param name="unambiguous_score" argument="-unambiguous_score" type="integer" optional="true" value="1000" label="Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated" help="(Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)"/> + <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="idxml"/> + <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> + <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> + <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> + </data> </outputs> - <help>Scores potential phosphorylation sites in order to localize the most probable sites. + <tests> + <expand macro="autotest_PhosphoScoring"/> + <expand macro="manutest_PhosphoScoring"/> + </tests> + <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites. -For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_PhosphoScoring.html</help> +For more information, visit http://www.openms.de/documentation/TOPP_PhosphoScoring.html]]></help> + <expand macro="references"/> </tool>