Mercurial > repos > galaxyp > openms_ticcalculator

comparison TICCalculator.xml @ 13:d623ad21ca59 draft

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 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:10:31 +0000
parents ed6c05e730de
children 5f36444a0f9d
comparison
equal deleted inserted replaced
12:4c263ca917ef 13:d623ad21ca59
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="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description> 5 <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">TICCalculator</token> 7 <token name="@EXECUTABLE@">TICCalculator</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@
36 <configfiles> 34 <configfiles>
37 <inputs name="args_json" data_style="paths"/> 35 <inputs name="args_json" data_style="paths"/>
38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 36 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 </configfiles> 37 </configfiles>
40 <inputs> 38 <inputs>
41 <param name="in" argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/> 39 <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" optional="false" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/>
42 <param name="read_method" argument="-read_method" type="select" optional="false" label="Method to read the file" help=""> 40 <param argument="-read_method" type="select" optional="true" label="Method to read the file" help="">
43 <option value="regular" selected="true">regular</option> 41 <option value="regular" selected="true">regular</option>
44 <option value="indexed">indexed</option> 42 <option value="indexed">indexed</option>
45 <option value="indexed_parallel">indexed_parallel</option> 43 <option value="indexed_parallel">indexed_parallel</option>
46 <option value="streaming">streaming</option> 44 <option value="streaming">streaming</option>
47 <option value="cached">cached</option> 45 <option value="cached">cached</option>
48 <option value="cached_parallel">cached_parallel</option> 46 <option value="cached_parallel">cached_parallel</option>
49 <expand macro="list_string_san"/> 47 <expand macro="list_string_san" name="read_method"/>
50 </param> 48 </param>
51 <param name="loadData" argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help=""/> 49 <param argument="-loadData" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Whether to actually load and decode the binary data (or whether to skip decoding the binary data)" help=""/>
52 <expand macro="adv_opts_macro"> 50 <expand macro="adv_opts_macro">
53 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 51 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
54 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 52 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
55 <expand macro="list_string_san"/> 53 <expand macro="list_string_san" name="test"/>
56 </param> 54 </param>
57 </expand> 55 </expand>
58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 56 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 57 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
60 </param> 58 </param>
65 </data> 63 </data>
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
68 </data> 66 </data>
69 </outputs> 67 </outputs>
70 <tests> 68 <tests><!-- UTILS_TICCalculator_1 -->
71 <expand macro="autotest_TICCalculator"/> 69 <test expect_num_outputs="1">
72 <expand macro="manutest_TICCalculator"/> 70 <section name="adv_opts">
71 <param name="force" value="false"/>
72 <param name="test" value="true"/>
73 </section>
74 <param name="in" value="MapNormalizer_output.mzML"/>
75 <param name="read_method" value="regular"/>
76 <param name="loadData" value="true"/>
77 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
78 <output name="ctd_out" ftype="xml">
79 <assert_contents>
80 <is_valid_xml/>
81 </assert_contents>
82 </output>
83 </test>
84 <!-- UTILS_TICCalculator_2 -->
85 <test expect_num_outputs="1">
86 <section name="adv_opts">
87 <param name="force" value="false"/>
88 <param name="test" value="true"/>
89 </section>
90 <param name="in" value="MapNormalizer_output.mzML"/>
91 <param name="read_method" value="streaming"/>
92 <param name="loadData" value="true"/>
93 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
94 <output name="ctd_out" ftype="xml">
95 <assert_contents>
96 <is_valid_xml/>
97 </assert_contents>
98 </output>
99 </test>
100 <!-- UTILS_TICCalculator_3 -->
101 <test expect_num_outputs="1">
102 <section name="adv_opts">
103 <param name="force" value="false"/>
104 <param name="test" value="true"/>
105 </section>
106 <param name="in" value="MapNormalizer_output.mzML"/>
107 <param name="read_method" value="streaming"/>
108 <param name="loadData" value="false"/>
109 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
110 <output name="ctd_out" ftype="xml">
111 <assert_contents>
112 <is_valid_xml/>
113 </assert_contents>
114 </output>
115 </test>
116 <!-- UTILS_TICCalculator_4 -->
117 <test expect_num_outputs="1">
118 <section name="adv_opts">
119 <param name="force" value="false"/>
120 <param name="test" value="true"/>
121 </section>
122 <param name="in" value="MapNormalizer_output.mzML"/>
123 <param name="read_method" value="indexed"/>
124 <param name="loadData" value="true"/>
125 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
126 <output name="ctd_out" ftype="xml">
127 <assert_contents>
128 <is_valid_xml/>
129 </assert_contents>
130 </output>
131 </test>
132 <!-- UTILS_TICCalculator_5 -->
133 <test expect_num_outputs="1">
134 <section name="adv_opts">
135 <param name="force" value="false"/>
136 <param name="test" value="true"/>
137 </section>
138 <param name="in" value="MapNormalizer_output.mzML"/>
139 <param name="read_method" value="indexed_parallel"/>
140 <param name="loadData" value="true"/>
141 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
142 <output name="ctd_out" ftype="xml">
143 <assert_contents>
144 <is_valid_xml/>
145 </assert_contents>
146 </output>
147 </test>
73 </tests> 148 </tests>
74 <help><![CDATA[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). 149 <help><![CDATA[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
75 150
76 151
77 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_TICCalculator.html]]></help> 152 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TICCalculator.html]]></help>
78 <expand macro="references"/> 153 <expand macro="references"/>
79 </tool> 154 </tool>