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comparison ExternalCalibration.xml @ 15:8bdbd9b42f3e 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 21:38:02 +0000
parents 1168fee85066
children
comparison
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14:1168fee85066 15:8bdbd9b42f3e
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: [Signal processing and preprocessing]--> 2 <!--Proposed Tool Section: [Mass Correction and Calibration]-->
4 <tool id="ExternalCalibration" name="ExternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="ExternalCalibration" name="ExternalCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies an external mass recalibration.</description> 4 <description>Applies an external mass recalibration</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">ExternalCalibration</token> 6 <token name="@EXECUTABLE@">ExternalCalibration</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 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="mzml" optional="false" label="Input peak file" help=" select mzml data sets(s)"/> 41 <param argument="-in" type="data" format="mzml" label="Input peak file" help=" select mzml data sets(s)"/>
43 <param argument="-offset" type="float" optional="true" value="0.0" label="Mass offset in ppm" help=""/> 42 <param argument="-offset" type="float" value="0.0" label="Mass offset in ppm" help=""/>
44 <param argument="-slope" type="float" optional="true" value="0.0" label="Slope (dependent on m/z)" help=""/> 43 <param argument="-slope" type="float" value="0.0" label="Slope (dependent on m/z)" help=""/>
45 <param argument="-power" type="float" optional="true" value="0.0" label="Power (dependent on m/z)" help=""/> 44 <param argument="-power" type="float" value="0.0" label="Power (dependent on m/z)" help=""/>
46 <param argument="-ms_level" type="text" optional="true" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)"> 45 <param argument="-ms_level" type="text" value="1 2 3" label="Target MS levels to apply the transformation onto" help="Scans with other levels remain unchanged (space separated list, in order to allow for spaces in list items surround them by single quotes)">
47 <expand macro="list_integer_valsan" name="ms_level"/> 46 <expand macro="list_integer_valsan" name="ms_level"/>
48 </param> 47 </param>
49 <expand macro="adv_opts_macro"> 48 <expand macro="adv_opts_macro">
50 <param 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=""/>
51 <param 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" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
52 <expand macro="list_string_san" name="test"/> 51 <expand macro="list_string_san" name="test"/>
53 </param> 52 </param>
54 </expand> 53 </expand>
55 <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">
56 <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>
60 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 59 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
61 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
62 <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>
63 </data> 62 </data>
64 </outputs> 63 </outputs>
65 <tests><!-- TOPP_ExternalCalibration_1_MS1 --> 64 <tests>
65 <!-- TOPP_ExternalCalibration_1_MS1 -->
66 <test expect_num_outputs="2"> 66 <test expect_num_outputs="2">
67 <section name="adv_opts"> 67 <section name="adv_opts">
68 <param name="force" value="false"/> 68 <param name="force" value="false"/>
69 <param name="test" value="true"/> 69 <param name="test" value="true"/>
70 </section> 70 </section>
71 <param name="in" value="ExternalCalibration_1_input.mzML"/> 71 <param name="in" value="ExternalCalibration_1_input.mzML"/>
72 <output name="out" file="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 72 <output name="out" value="ExternalCalibration_1_MS1_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
73 <param name="offset" value="-5.5"/> 73 <param name="offset" value="-5.5"/>
74 <param name="slope" value="0.0001"/> 74 <param name="slope" value="0.0001"/>
75 <param name="power" value="0.0"/> 75 <param name="power" value="0.0"/>
76 <param name="ms_level" value="1"/> 76 <param name="ms_level" value="1"/>
77 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 77 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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 <!-- TOPP_ExternalCalibration_2_MS2 --> 87 <!-- TOPP_ExternalCalibration_2_MS2 -->
85 <test expect_num_outputs="2"> 88 <test expect_num_outputs="2">
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>
90 <param name="in" value="ExternalCalibration_1_input.mzML"/> 93 <param name="in" value="ExternalCalibration_1_input.mzML"/>
91 <output name="out" file="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/> 94 <output name="out" value="ExternalCalibration_2_MS2_out.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
92 <param name="offset" value="-5.5"/> 95 <param name="offset" value="-5.5"/>
93 <param name="slope" value="0.0001"/> 96 <param name="slope" value="0.0001"/>
94 <param name="power" value="0.0"/> 97 <param name="power" value="0.0"/>
95 <param name="ms_level" value="2"/> 98 <param name="ms_level" value="2"/>
96 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 99 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
97 <output name="ctd_out" ftype="xml"> 100 <output name="ctd_out" ftype="xml">
98 <assert_contents> 101 <assert_contents>
99 <is_valid_xml/> 102 <is_valid_xml/>
100 </assert_contents> 103 </assert_contents>
101 </output> 104 </output>
105 <assert_stdout>
106 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
107 </assert_stdout>
102 </test> 108 </test>
103 </tests> 109 </tests>
104 <help><![CDATA[Applies an external mass recalibration. 110 <help><![CDATA[Applies an external mass recalibration.
105 111
106 112
107 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_ExternalCalibration.html]]></help> 113 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_ExternalCalibration.html]]></help>
108 <expand macro="references"/> 114 <expand macro="references"/>
109 </tool> 115 </tool>