Mercurial > repos > galaxyp > openms_idconflictresolver

comparison IDConflictResolver.xml @ 16:5c9e1b5d3b95 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:41:35 +0000
parents ca1740533b59
children
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15:ca1740533b59 16:5c9e1b5d3b95
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: [ID Processing]--> 2 <!--Proposed Tool Section: [Identification Processing]-->
4 <tool id="IDConflictResolver" name="IDConflictResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Resolves ambiguous annotations of features with peptide identifications</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">IDConflictResolver</token> 6 <token name="@EXECUTABLE@">IDConflictResolver</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="consensusxml,featurexml" optional="false" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/> 41 <param argument="-in" type="data" format="consensusxml,featurexml" label="Input file (data annotated with identifications)" help=" select consensusxml,featurexml data sets(s)"/>
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"> 42 <param argument="-resolve_between_features" type="select" 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">
44 <option value="off" selected="true">off</option> 43 <option value="off" selected="true">off</option>
45 <option value="highest_intensity">highest_intensity</option> 44 <option value="highest_intensity">highest_intensity</option>
46 <expand macro="list_string_san" name="resolve_between_features"/> 45 <expand macro="list_string_san" name="resolve_between_features"/>
47 </param> 46 </param>
48 <expand macro="adv_opts_macro"> 47 <expand macro="adv_opts_macro">
49 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 48 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
50 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 49 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
51 <expand macro="list_string_san" name="test"/> 50 <expand macro="list_string_san" name="test"/>
52 </param> 51 </param>
53 </expand> 52 </expand>
54 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 53 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
55 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 54 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
59 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/> 58 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 59 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
61 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 60 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
62 </data> 61 </data>
63 </outputs> 62 </outputs>
64 <tests><!-- TOPP_IDConflictResolver_1 --> 63 <tests>
64 <!-- TOPP_IDConflictResolver_1 -->
65 <test expect_num_outputs="2"> 65 <test expect_num_outputs="2">
66 <section name="adv_opts"> 66 <section name="adv_opts">
67 <param name="force" value="false"/> 67 <param name="force" value="false"/>
68 <param name="test" value="true"/> 68 <param name="test" value="true"/>
69 </section> 69 </section>
70 <param name="in" value="IDConflictResolver_1_input.featureXML"/> 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"/> 71 <output name="out" value="IDConflictResolver_1_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
72 <param name="resolve_between_features" value="off"/> 72 <param name="resolve_between_features" value="off"/>
73 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 73 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
74 <output name="ctd_out" ftype="xml"> 74 <output name="ctd_out" ftype="xml">
75 <assert_contents> 75 <assert_contents>
76 <is_valid_xml/> 76 <is_valid_xml/>
77 </assert_contents> 77 </assert_contents>
78 </output> 78 </output>
79 <assert_stdout>
80 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
81 </assert_stdout>
79 </test> 82 </test>
80 <!-- TOPP_IDConflictResolver_2 --> 83 <!-- TOPP_IDConflictResolver_2 -->
81 <test expect_num_outputs="2"> 84 <test expect_num_outputs="2">
82 <section name="adv_opts"> 85 <section name="adv_opts">
83 <param name="force" value="false"/> 86 <param name="force" value="false"/>
84 <param name="test" value="true"/> 87 <param name="test" value="true"/>
85 </section> 88 </section>
86 <param name="in" value="IDConflictResolver_2_input.consensusXML"/> 89 <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"/> 90 <output name="out" value="IDConflictResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
88 <param name="resolve_between_features" value="off"/> 91 <param name="resolve_between_features" value="off"/>
89 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 92 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
90 <output name="ctd_out" ftype="xml"> 93 <output name="ctd_out" ftype="xml">
91 <assert_contents> 94 <assert_contents>
92 <is_valid_xml/> 95 <is_valid_xml/>
93 </assert_contents> 96 </assert_contents>
94 </output> 97 </output>
98 <assert_stdout>
99 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
100 </assert_stdout>
95 </test> 101 </test>
96 <!-- TOPP_IDConflictResolver_3 --> 102 <!-- TOPP_IDConflictResolver_3 -->
97 <test expect_num_outputs="2"> 103 <test expect_num_outputs="2">
98 <section name="adv_opts"> 104 <section name="adv_opts">
99 <param name="force" value="false"/> 105 <param name="force" value="false"/>
100 <param name="test" value="true"/> 106 <param name="test" value="true"/>
101 </section> 107 </section>
102 <param name="in" value="IDConflictResolver_3_input.consensusXML"/> 108 <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"/> 109 <output name="out" value="IDConflictResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
104 <param name="resolve_between_features" value="off"/> 110 <param name="resolve_between_features" value="off"/>
105 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 111 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
106 <output name="ctd_out" ftype="xml"> 112 <output name="ctd_out" ftype="xml">
107 <assert_contents> 113 <assert_contents>
108 <is_valid_xml/> 114 <is_valid_xml/>
109 </assert_contents> 115 </assert_contents>
110 </output> 116 </output>
117 <assert_stdout>
118 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
119 </assert_stdout>
111 </test> 120 </test>
112 <!-- TOPP_IDConflictResolver_4 --> 121 <!-- TOPP_IDConflictResolver_4 -->
113 <test expect_num_outputs="2"> 122 <test expect_num_outputs="2">
114 <section name="adv_opts"> 123 <section name="adv_opts">
115 <param name="force" value="false"/> 124 <param name="force" value="false"/>
116 <param name="test" value="true"/> 125 <param name="test" value="true"/>
117 </section> 126 </section>
118 <param name="in" value="IDConflictResolver_4_input.featureXML"/> 127 <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"/> 128 <output name="out" value="IDConflictResolver_4_output.featureXML" compare="sim_size" delta_frac="0.7" ftype="featurexml"/>
120 <param name="resolve_between_features" value="highest_intensity"/> 129 <param name="resolve_between_features" value="highest_intensity"/>
121 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 130 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
122 <output name="ctd_out" ftype="xml"> 131 <output name="ctd_out" ftype="xml">
123 <assert_contents> 132 <assert_contents>
124 <is_valid_xml/> 133 <is_valid_xml/>
125 </assert_contents> 134 </assert_contents>
126 </output> 135 </output>
136 <assert_stdout>
137 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
138 </assert_stdout>
127 </test> 139 </test>
128 </tests> 140 </tests>
129 <help><![CDATA[Resolves ambiguous annotations of features with peptide identifications 141 <help><![CDATA[Resolves ambiguous annotations of features with peptide identifications
130 142
131 143
132 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDConflictResolver.html]]></help> 144 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDConflictResolver.html]]></help>
133 <expand macro="references"/> 145 <expand macro="references"/>
134 </tool> 146 </tool>