Mercurial > repos > galaxyp > openms_phosphoscoring

comparison PhosphoScoring.xml @ 13:996ca7c1d45e draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:08:12 +0000
parents c04ff2777ed2
children
comparison
equal deleted inserted replaced
12:236b61e62648 13:996ca7c1d45e
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="PhosphoScoring" name="PhosphoScoring" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description> 5 <description>Scores potential phosphorylation sites in order to localize the most probable sites.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PhosphoScoring</token> 7 <token name="@EXECUTABLE@">PhosphoScoring</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/> 46 <param argument="-in" type="data" format="mzml" optional="false" label="Input file with MS/MS spectra" help=" select mzml data sets(s)"/>
49 <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)"/> 47 <param 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)"/>
50 <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=""/> 48 <param argument="-fragment_mass_tolerance" type="float" optional="true" min="0.0" value="0.05" label="Fragment mass tolerance for spectrum comparisons" help=""/>
51 <param name="fragment_mass_unit" argument="-fragment_mass_unit" display="radio" type="select" optional="false" label="Unit of fragment mass tolerance" help=""> 49 <param argument="-fragment_mass_unit" type="select" optional="true" label="Unit of fragment mass tolerance" help="">
52 <option value="Da" selected="true">Da</option> 50 <option value="Da" selected="true">Da</option>
53 <option value="ppm">ppm</option> 51 <option value="ppm">ppm</option>
54 <expand macro="list_string_san"/> 52 <expand macro="list_string_san" name="fragment_mass_unit"/>
55 </param> 53 </param>
56 <expand macro="adv_opts_macro"> 54 <expand macro="adv_opts_macro">
57 <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=""/> 55 <param 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=""/>
58 <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=""/> 56 <param 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=""/>
59 <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'.)"/> 57 <param 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'.)"/>
60 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 58 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
61 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 59 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
62 <expand macro="list_string_san"/> 60 <expand macro="list_string_san" name="test"/>
63 </param> 61 </param>
64 </expand> 62 </expand>
65 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 63 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
66 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 64 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
67 </param> 65 </param>
70 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 68 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
71 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
72 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 70 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
73 </data> 71 </data>
74 </outputs> 72 </outputs>
75 <tests> 73 <tests><test expect_num_outputs="1"><!-- same input as used in the MSGF+Adapter -->
76 <expand macro="autotest_PhosphoScoring"/> 74 <param name="adv_opts|test" value="true"/>
77 <expand macro="manutest_PhosphoScoring"/> 75 <param name="in" ftype="mzml" value="spectra.mzML"/>
78 </tests> 76 <param name="id" ftype="idxml" value="MSGFPlusAdapter_1_out1.tmp"/>
77 <output name="out" ftype="idxml" value="PhosphoScoring.idxml" compare="sim_size" delta="5700"/>
78 </test>
79 </tests>
79 <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites. 80 <help><![CDATA[Scores potential phosphorylation sites in order to localize the most probable sites.
80 81
81 82
82 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_PhosphoScoring.html]]></help> 83 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_PhosphoScoring.html]]></help>
83 <expand macro="references"/> 84 <expand macro="references"/>
84 </tool> 85 </tool>