Mercurial > repos > galaxyp > openms_idscoreswitcher

comparison IDScoreSwitcher.xml @ 14:5a56ed4fb4c2 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:29:53 +0000
parents 4204882495f2
children
comparison
equal deleted inserted replaced
13:4204882495f2 14:5a56ed4fb4c2
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.--> 1 <!--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]--> 2 <!--Proposed Tool Section: [Identification Processing]-->
4 <tool id="IDScoreSwitcher" name="IDScoreSwitcher" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Switches between different scores of peptide or protein hits in identification data</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">IDScoreSwitcher</token> 6 <token name="@EXECUTABLE@">IDScoreSwitcher</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
13 @EXT_FOO@ 12 @EXT_FOO@
14 #import re 13 #import re
15 14
16 ## Preprocessing 15 ## Preprocessing
17 mkdir in && 16 mkdir in &&
18 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' && 17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
19 mkdir out && 18 mkdir out &&
20 19
21 ## Main program call 20 ## Main program call
22 21
23 set -o pipefail && 22 set -o pipefail &&
37 <configfiles> 36 <configfiles>
38 <inputs name="args_json" data_style="paths"/> 37 <inputs name="args_json" data_style="paths"/>
39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
40 </configfiles> 39 </configfiles>
41 <inputs> 40 <inputs>
42 <param argument="-in" type="data" format="idxml" optional="false" label="Input file" help=" select idxml data sets(s)"/> 41 <param argument="-in" type="data" format="idxml" label="Input file" help=" select idxml data sets(s)"/>
43 <param argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
44 <param argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help=""> 42 <param argument="-new_score" type="text" optional="true" value="" label="Name of the meta value to use as the new score" help="">
45 <expand macro="list_string_san" name="new_score"/> 43 <expand macro="list_string_san" name="new_score"/>
46 </param> 44 </param>
47 <param argument="-new_score_orientation" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help=""> 45 <param argument="-new_score_orientation" type="select" optional="true" label="Orientation of the new score (are higher or lower values better?)" help="">
48 <option value="lower_better">lower_better</option> 46 <option value="lower_better">lower_better</option>
53 <expand macro="list_string_san" name="new_score_type"/> 51 <expand macro="list_string_san" name="new_score_type"/>
54 </param> 52 </param>
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=""> 53 <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="">
56 <expand macro="list_string_san" name="old_score"/> 54 <expand macro="list_string_san" name="old_score"/>
57 </param> 55 </param>
56 <param argument="-proteins" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Apply to protein scores instead of PSM scores" help=""/>
58 <expand macro="adv_opts_macro"> 57 <expand macro="adv_opts_macro">
59 <param 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=""/>
60 <param 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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
61 <expand macro="list_string_san" name="test"/> 60 <expand macro="list_string_san" name="test"/>
62 </param> 61 </param>
63 </expand> 62 </expand>
64 <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">
65 <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>
69 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 68 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
70 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 69 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
71 <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>
72 </data> 71 </data>
73 </outputs> 72 </outputs>
74 <tests><!-- UTILS_IDScoreSwitcher_1 --> 73 <tests>
74 <!-- TOPP_IDScoreSwitcher_1 -->
75 <test expect_num_outputs="2"> 75 <test expect_num_outputs="2">
76 <section name="adv_opts"> 76 <section name="adv_opts">
77 <param name="force" value="false"/> 77 <param name="force" value="false"/>
78 <param name="test" value="true"/> 78 <param name="test" value="true"/>
79 </section> 79 </section>
80 <param name="in" value="IDFileConverter_12_output.idXML"/> 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"/> 81 <output name="out" value="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"/> 82 <param name="new_score" value="Percolator_PEP"/>
84 <param name="new_score_orientation" value="lower_better"/> 83 <param name="new_score_orientation" value="lower_better"/>
85 <param name="new_score_type" value="Posterior Error Probability"/> 84 <param name="new_score_type" value="Posterior Error Probability"/>
86 <param name="old_score" value="Percolator_qvalue"/> 85 <param name="old_score" value="Percolator_qvalue"/>
86 <param name="proteins" value="false"/>
87 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 87 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
88 <output name="ctd_out" ftype="xml"> 88 <output name="ctd_out" ftype="xml">
89 <assert_contents> 89 <assert_contents>
90 <is_valid_xml/> 90 <is_valid_xml/>
91 </assert_contents> 91 </assert_contents>
92 </output> 92 </output>
93 <assert_stdout>
94 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
95 </assert_stdout>
93 </test> 96 </test>
94 <!-- UTILS_IDScoreSwitcher_2 --> 97 <!-- TOPP_IDScoreSwitcher_2 -->
95 <test expect_num_outputs="2"> 98 <test expect_num_outputs="2">
96 <section name="adv_opts"> 99 <section name="adv_opts">
97 <param name="force" value="false"/> 100 <param name="force" value="false"/>
98 <param name="test" value="true"/> 101 <param name="test" value="true"/>
99 </section> 102 </section>
100 <param name="in" value="IDScoreSwitcher_2_input.idXML"/> 103 <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"/> 104 <output name="out" value="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"/> 105 <param name="new_score" value="Posterior Probability_score"/>
104 <param name="new_score_orientation" value="higher_better"/> 106 <param name="new_score_orientation" value="higher_better"/>
105 <param name="new_score_type" value="Posterior Probability"/> 107 <param name="new_score_type" value="Posterior Probability"/>
106 <param name="old_score" value=""/> 108 <param name="old_score" value=""/>
109 <param name="proteins" value="true"/>
107 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 110 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
108 <output name="ctd_out" ftype="xml"> 111 <output name="ctd_out" ftype="xml">
109 <assert_contents> 112 <assert_contents>
110 <is_valid_xml/> 113 <is_valid_xml/>
111 </assert_contents> 114 </assert_contents>
112 </output> 115 </output>
116 <assert_stdout>
117 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
118 </assert_stdout>
113 </test> 119 </test>
114 </tests> 120 </tests>
115 <help><![CDATA[Switches between different scores of peptide or protein hits in identification data 121 <help><![CDATA[Switches between different scores of peptide or protein hits in identification data
116 122
117 123
118 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDScoreSwitcher.html]]></help> 124 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDScoreSwitcher.html]]></help>
119 <expand macro="references"/> 125 <expand macro="references"/>
120 </tool> 126 </tool>