Mercurial > repos > galaxyp > openms_idscoreswitcher
comparison IDScoreSwitcher.xml @ 13:4204882495f2 draft
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 19:20:22 +0000 |
parents | ec0d05b20eed |
children | 5a56ed4fb4c2 |
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12:be74a8cd7d66 | 13:4204882495f2 |
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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: [Utilities]--> | 3 <!--Proposed Tool Section: [Utilities]--> |
4 <tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Switches between different scores of peptide or protein hits in identification data</description> | 5 <description>Switches between different scores of peptide or protein hits in identification data</description> |
6 <macros> | 6 <macros> |
7 <token name="@EXECUTABLE@">IDScoreSwitcher</token> | 7 <token name="@EXECUTABLE@">IDScoreSwitcher</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@ |
39 <configfiles> | 37 <configfiles> |
40 <inputs name="args_json" data_style="paths"/> | 38 <inputs name="args_json" data_style="paths"/> |
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
42 </configfiles> | 40 </configfiles> |
43 <inputs> | 41 <inputs> |
44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/> | 42 <param argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/> |
45 <param name="proteins" argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/> | 43 <param argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/> |
46 <param name="new_score" argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help=""> | 44 <param argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help=""> |
47 <expand macro="list_string_san"/> | 45 <expand macro="list_string_san" name="new_score"/> |
48 </param> | 46 </param> |
49 <param name="new_score_orientation" argument="-new_score_orientation" display="radio" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help=""> | 47 <param argument="-new_score_orientation" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help=""> |
50 <option value="">default (nothing chosen)</option> | |
51 <option value="lower_better">lower_better</option> | 48 <option value="lower_better">lower_better</option> |
52 <option value="higher_better">higher_better</option> | 49 <option value="higher_better">higher_better</option> |
53 <expand macro="list_string_san"/> | 50 <expand macro="list_string_san" name="new_score_orientation"/> |
54 </param> | 51 </param> |
55 <param name="new_score_type" argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help=""> | 52 <param argument="-new_score_type" type="text" optional="true" value="" label="Name to use as the type of the new score (default: same as 'new_score')" help=""> |
56 <expand macro="list_string_san"/> | 53 <expand macro="list_string_san" name="new_score_type"/> |
57 </param> | 54 </param> |
58 <param name="old_score" argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help=""> | 55 <param argument="-old_score" type="text" optional="true" value="" label="Name to use for the meta value storing the old score (default: old score type)" help=""> |
59 <expand macro="list_string_san"/> | 56 <expand macro="list_string_san" name="old_score"/> |
60 </param> | 57 </param> |
61 <expand macro="adv_opts_macro"> | 58 <expand macro="adv_opts_macro"> |
62 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 59 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
63 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 60 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> |
64 <expand macro="list_string_san"/> | 61 <expand macro="list_string_san" name="test"/> |
65 </param> | 62 </param> |
66 </expand> | 63 </expand> |
67 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 64 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
68 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 65 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
69 </param> | 66 </param> |
72 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> | 69 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> |
73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 70 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 71 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
75 </data> | 72 </data> |
76 </outputs> | 73 </outputs> |
77 <tests> | 74 <tests><!-- UTILS_IDScoreSwitcher_1 --> |
78 <expand macro="autotest_IDScoreSwitcher"/> | 75 <test expect_num_outputs="2"> |
79 <expand macro="manutest_IDScoreSwitcher"/> | 76 <section name="adv_opts"> |
77 <param name="force" value="false"/> | |
78 <param name="test" value="true"/> | |
79 </section> | |
80 <param name="in" value="IDFileConverter_12_output.idXML"/> | |
81 <output name="out" file="IDFileConverter_13_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> | |
82 <param name="proteins" value="false"/> | |
83 <param name="new_score" value="Percolator_PEP"/> | |
84 <param name="new_score_orientation" value="lower_better"/> | |
85 <param name="new_score_type" value="Posterior Error Probability"/> | |
86 <param name="old_score" value="Percolator_qvalue"/> | |
87 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
88 <output name="ctd_out" ftype="xml"> | |
89 <assert_contents> | |
90 <is_valid_xml/> | |
91 </assert_contents> | |
92 </output> | |
93 </test> | |
94 <!-- UTILS_IDScoreSwitcher_2 --> | |
95 <test expect_num_outputs="2"> | |
96 <section name="adv_opts"> | |
97 <param name="force" value="false"/> | |
98 <param name="test" value="true"/> | |
99 </section> | |
100 <param name="in" value="IDScoreSwitcher_2_input.idXML"/> | |
101 <output name="out" file="IDScoreSwitcher_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> | |
102 <param name="proteins" value="true"/> | |
103 <param name="new_score" value="Posterior Probability_score"/> | |
104 <param name="new_score_orientation" value="higher_better"/> | |
105 <param name="new_score_type" value="Posterior Probability"/> | |
106 <param name="old_score" value=""/> | |
107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> | |
108 <output name="ctd_out" ftype="xml"> | |
109 <assert_contents> | |
110 <is_valid_xml/> | |
111 </assert_contents> | |
112 </output> | |
113 </test> | |
80 </tests> | 114 </tests> |
81 <help><![CDATA[Switches between different scores of peptide or protein hits in identification data | 115 <help><![CDATA[Switches between different scores of peptide or protein hits in identification data |
82 | 116 |
83 | 117 |
84 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDScoreSwitcher.html]]></help> | 118 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDScoreSwitcher.html]]></help> |
85 <expand macro="references"/> | 119 <expand macro="references"/> |
86 </tool> | 120 </tool> |