Mercurial > repos > galaxyp > openms_idconflictresolver

comparison IDConflictResolver.xml @ 15:ca1740533b59 draft

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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 19:09:05 +0000
parents fb0e6f70a1df
children 5c9e1b5d3b95
comparison
equal deleted inserted replaced
14:c28f13cab67a 15:ca1740533b59
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="IDConflictResolver" name="IDConflictResolver" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="IDConflictResolver" name="IDConflictResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Resolves ambiguous annotations of features with peptide identifications</description> 5 <description>Resolves ambiguous annotations of features with peptide identifications</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDConflictResolver</token> 7 <token name="@EXECUTABLE@">IDConflictResolver</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="consensusxml,featurexml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/> 42 <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/>
45 <param name="resolve_between_features" argument="-resolve_between_features" display="radio" type="select" optional="false" label="A map may contain multiple features with both identical (possibly modified" help="i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence"> 43 <param argument="-resolve_between_features" type="select" optional="true" label="A map may contain multiple features with both identical (possibly modified" help="i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence">
46 <option value="off" selected="true">off</option> 44 <option value="off" selected="true">off</option>
47 <option value="highest_intensity">highest_intensity</option> 45 <option value="highest_intensity">highest_intensity</option>
48 <expand macro="list_string_san"/> 46 <expand macro="list_string_san" name="resolve_between_features"/>
49 </param> 47 </param>
50 <expand macro="adv_opts_macro"> 48 <expand macro="adv_opts_macro">
51 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 49 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
52 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 50 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
53 <expand macro="list_string_san"/> 51 <expand macro="list_string_san" name="test"/>
54 </param> 52 </param>
55 </expand> 53 </expand>
56 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
57 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
58 </param> 56 </param>
61 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/> 59 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 61 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
64 </data> 62 </data>
65 </outputs> 63 </outputs>
66 <tests> 64 <tests><!-- TOPP_IDConflictResolver_1 -->
67 <expand macro="autotest_IDConflictResolver"/> 65 <test expect_num_outputs="2">
68 <expand macro="manutest_IDConflictResolver"/> 66 <section name="adv_opts">
67 <param name="force" value="false"/>
68 <param name="test" value="true"/>
69 </section>
70 <param name="in" value="IDConflictResolver_1_input.featureXML"/>
71 <output name="out" file="IDConflictResolver_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
72 <param name="resolve_between_features" value="off"/>
73 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
74 <output name="ctd_out" ftype="xml">
75 <assert_contents>
76 <is_valid_xml/>
77 </assert_contents>
78 </output>
79 </test>
80 <!-- TOPP_IDConflictResolver_2 -->
81 <test expect_num_outputs="2">
82 <section name="adv_opts">
83 <param name="force" value="false"/>
84 <param name="test" value="true"/>
85 </section>
86 <param name="in" value="IDConflictResolver_2_input.consensusXML"/>
87 <output name="out" file="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
88 <param name="resolve_between_features" value="off"/>
89 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
90 <output name="ctd_out" ftype="xml">
91 <assert_contents>
92 <is_valid_xml/>
93 </assert_contents>
94 </output>
95 </test>
96 <!-- TOPP_IDConflictResolver_3 -->
97 <test expect_num_outputs="2">
98 <section name="adv_opts">
99 <param name="force" value="false"/>
100 <param name="test" value="true"/>
101 </section>
102 <param name="in" value="IDConflictResolver_3_input.consensusXML"/>
103 <output name="out" file="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
104 <param name="resolve_between_features" value="off"/>
105 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
106 <output name="ctd_out" ftype="xml">
107 <assert_contents>
108 <is_valid_xml/>
109 </assert_contents>
110 </output>
111 </test>
112 <!-- TOPP_IDConflictResolver_4 -->
113 <test expect_num_outputs="2">
114 <section name="adv_opts">
115 <param name="force" value="false"/>
116 <param name="test" value="true"/>
117 </section>
118 <param name="in" value="IDConflictResolver_4_input.featureXML"/>
119 <output name="out" file="IDConflictResolver_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
120 <param name="resolve_between_features" value="highest_intensity"/>
121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
122 <output name="ctd_out" ftype="xml">
123 <assert_contents>
124 <is_valid_xml/>
125 </assert_contents>
126 </output>
127 </test>
69 </tests> 128 </tests>
70 <help><![CDATA[Resolves ambiguous annotations of features with peptide identifications 129 <help><![CDATA[Resolves ambiguous annotations of features with peptide identifications
71 130
72 131
73 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDConflictResolver.html]]></help> 132 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDConflictResolver.html]]></help>
74 <expand macro="references"/> 133 <expand macro="references"/>
75 </tool> 134 </tool>