Mercurial > repos > galaxyp > openms_phosphoscoring
comparison PhosphoScoring.xml @ 13:996ca7c1d45e draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:08:12 +0000 |
parents | c04ff2777ed2 |
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12:236b61e62648 | 13:996ca7c1d45e |
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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> |