Mercurial > repos > galaxyp > openms_ticcalculator

comparison TICCalculator.xml @ 14:5f36444a0f9d 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 21:43:12 +0000
parents d623ad21ca59
children
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13:d623ad21ca59 14:5f36444a0f9d
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: []-->
4 <tool id="TICCalculator" name="TICCalculator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Calculates the TIC from a mass spectrometric raw file (useful for benchmarking)</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">TICCalculator</token> 6 <token name="@EXECUTABLE@">TICCalculator</token>
8 <import>macros.xml</import> 7 <import>macros.xml</import>
9 </macros> 8 </macros>
10 <expand macro="requirements"/> 9 <expand macro="requirements"/>
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 18
20 ## Main program call 19 ## Main program call
21 20
22 set -o pipefail && 21 set -o pipefail &&
23 @EXECUTABLE@ -write_ctd ./ && 22 @EXECUTABLE@ -write_ctd ./ &&
34 <configfiles> 33 <configfiles>
35 <inputs name="args_json" data_style="paths"/> 34 <inputs name="args_json" data_style="paths"/>
36 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 35 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
37 </configfiles> 36 </configfiles>
38 <inputs> 37 <inputs>
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)"/> 38 <param argument="-in" type="data" format="consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular" label="Input file to convert" help=" select consensusxml,dta,dta2d,edta,featurexml,kroenik,mgf,ms2,mzdata,mzml,mzxml,peplist,tabular data sets(s)"/>
40 <param argument="-read_method" type="select" optional="true" label="Method to read the file" help=""> 39 <param argument="-read_method" type="select" label="Method to read the file" help="">
41 <option value="regular" selected="true">regular</option> 40 <option value="regular" selected="true">regular</option>
42 <option value="indexed">indexed</option> 41 <option value="indexed">indexed</option>
43 <option value="indexed_parallel">indexed_parallel</option> 42 <option value="indexed_parallel">indexed_parallel</option>
44 <option value="streaming">streaming</option> 43 <option value="streaming">streaming</option>
45 <option value="cached">cached</option> 44 <option value="cached">cached</option>
47 <expand macro="list_string_san" name="read_method"/> 46 <expand macro="list_string_san" name="read_method"/>
48 </param> 47 </param>
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=""/> 48 <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=""/>
50 <expand macro="adv_opts_macro"> 49 <expand macro="adv_opts_macro">
51 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 50 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
52 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 51 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
53 <expand macro="list_string_san" name="test"/> 52 <expand macro="list_string_san" name="test"/>
54 </param> 53 </param>
55 </expand> 54 </expand>
56 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 55 <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> 56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
63 </data> 62 </data>
64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 64 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
66 </data> 65 </data>
67 </outputs> 66 </outputs>
68 <tests><!-- UTILS_TICCalculator_1 --> 67 <tests>
68 <!-- TOPP_TICCalculator_1 -->
69 <test expect_num_outputs="1"> 69 <test expect_num_outputs="1">
70 <section name="adv_opts"> 70 <section name="adv_opts">
71 <param name="force" value="false"/> 71 <param name="force" value="false"/>
72 <param name="test" value="true"/> 72 <param name="test" value="true"/>
73 </section> 73 </section>
78 <output name="ctd_out" ftype="xml"> 78 <output name="ctd_out" ftype="xml">
79 <assert_contents> 79 <assert_contents>
80 <is_valid_xml/> 80 <is_valid_xml/>
81 </assert_contents> 81 </assert_contents>
82 </output> 82 </output>
83 <assert_stdout>
84 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
85 </assert_stdout>
83 </test> 86 </test>
84 <!-- UTILS_TICCalculator_2 --> 87 <!-- TOPP_TICCalculator_2 -->
85 <test expect_num_outputs="1"> 88 <test expect_num_outputs="1">
86 <section name="adv_opts"> 89 <section name="adv_opts">
87 <param name="force" value="false"/> 90 <param name="force" value="false"/>
88 <param name="test" value="true"/> 91 <param name="test" value="true"/>
89 </section> 92 </section>
94 <output name="ctd_out" ftype="xml"> 97 <output name="ctd_out" ftype="xml">
95 <assert_contents> 98 <assert_contents>
96 <is_valid_xml/> 99 <is_valid_xml/>
97 </assert_contents> 100 </assert_contents>
98 </output> 101 </output>
102 <assert_stdout>
103 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
104 </assert_stdout>
99 </test> 105 </test>
100 <!-- UTILS_TICCalculator_3 --> 106 <!-- TOPP_TICCalculator_3 -->
101 <test expect_num_outputs="1"> 107 <test expect_num_outputs="1">
102 <section name="adv_opts"> 108 <section name="adv_opts">
103 <param name="force" value="false"/> 109 <param name="force" value="false"/>
104 <param name="test" value="true"/> 110 <param name="test" value="true"/>
105 </section> 111 </section>
110 <output name="ctd_out" ftype="xml"> 116 <output name="ctd_out" ftype="xml">
111 <assert_contents> 117 <assert_contents>
112 <is_valid_xml/> 118 <is_valid_xml/>
113 </assert_contents> 119 </assert_contents>
114 </output> 120 </output>
121 <assert_stdout>
122 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
123 </assert_stdout>
115 </test> 124 </test>
116 <!-- UTILS_TICCalculator_4 --> 125 <!-- TOPP_TICCalculator_4 -->
117 <test expect_num_outputs="1"> 126 <test expect_num_outputs="1">
118 <section name="adv_opts"> 127 <section name="adv_opts">
119 <param name="force" value="false"/> 128 <param name="force" value="false"/>
120 <param name="test" value="true"/> 129 <param name="test" value="true"/>
121 </section> 130 </section>
126 <output name="ctd_out" ftype="xml"> 135 <output name="ctd_out" ftype="xml">
127 <assert_contents> 136 <assert_contents>
128 <is_valid_xml/> 137 <is_valid_xml/>
129 </assert_contents> 138 </assert_contents>
130 </output> 139 </output>
140 <assert_stdout>
141 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
142 </assert_stdout>
131 </test> 143 </test>
132 <!-- UTILS_TICCalculator_5 --> 144 <!-- TOPP_TICCalculator_5 -->
133 <test expect_num_outputs="1"> 145 <test expect_num_outputs="1">
134 <section name="adv_opts"> 146 <section name="adv_opts">
135 <param name="force" value="false"/> 147 <param name="force" value="false"/>
136 <param name="test" value="true"/> 148 <param name="test" value="true"/>
137 </section> 149 </section>
142 <output name="ctd_out" ftype="xml"> 154 <output name="ctd_out" ftype="xml">
143 <assert_contents> 155 <assert_contents>
144 <is_valid_xml/> 156 <is_valid_xml/>
145 </assert_contents> 157 </assert_contents>
146 </output> 158 </output>
159 <assert_stdout>
160 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
161 </assert_stdout>
147 </test> 162 </test>
148 </tests> 163 </tests>
149 <help><![CDATA[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking). 164 <help><![CDATA[Calculates the TIC from a mass spectrometric raw file (useful for benchmarking).
150 165
151 166
152 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_TICCalculator.html]]></help> 167 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_TICCalculator.html]]></help>
153 <expand macro="references"/> 168 <expand macro="references"/>
154 </tool> 169 </tool>