Mercurial > repos > galaxyp > openms_idrtcalibration

comparison IDRTCalibration.xml @ 15:f7226e34dc70 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 21:38:25 +0000
parents 7ff821b34ebc
children
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14:7ff821b34ebc 15:f7226e34dc70
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: [Mass Correction and Calibration]-->
4 <tool id="IDRTCalibration" name="IDRTCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="IDRTCalibration" name="IDRTCalibration" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description> 4 <description>Can be used to calibrate RTs of peptide hits linearly to standards</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">IDRTCalibration</token> 6 <token name="@EXECUTABLE@">IDRTCalibration</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="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> 41 <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
43 <param argument="-calibrant_1_reference" type="float" optional="true" value="0.1" label="The RT of the first calibrant in the reference file" help=""/> 42 <param argument="-calibrant_1_reference" type="float" value="0.1" label="The RT of the first calibrant in the reference file" help=""/>
44 <param argument="-calibrant_2_reference" type="float" optional="true" value="0.9" label="The RT of the second calibrant in the reference file" help=""/> 43 <param argument="-calibrant_2_reference" type="float" value="0.9" label="The RT of the second calibrant in the reference file" help=""/>
45 <param argument="-calibrant_1_input" type="float" optional="true" value="-1.0" label="The RT of the first calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> 44 <param argument="-calibrant_1_input" type="float" value="-1.0" label="The RT of the first calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/>
46 <param argument="-calibrant_2_input" type="float" optional="true" value="-1.0" label="The RT of the second calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/> 45 <param argument="-calibrant_2_input" type="float" value="-1.0" label="The RT of the second calibrant in the input file" help="Please note that this value needs to be set. The default value -1.0 is not allowed"/>
47 <expand macro="adv_opts_macro"> 46 <expand macro="adv_opts_macro">
48 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 47 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
49 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 48 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
50 <expand macro="list_string_san" name="test"/> 49 <expand macro="list_string_san" name="test"/>
51 </param> 50 </param>
52 </expand> 51 </expand>
53 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 52 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
54 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 53 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
58 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 57 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
59 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
60 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
61 </data> 60 </data>
62 </outputs> 61 </outputs>
63 <tests><!-- TOPP_IDRTCalibration_1 --> 62 <tests>
63 <!-- TOPP_IDRTCalibration_1 -->
64 <test expect_num_outputs="2"> 64 <test expect_num_outputs="2">
65 <section name="adv_opts"> 65 <section name="adv_opts">
66 <param name="force" value="false"/> 66 <param name="force" value="false"/>
67 <param name="test" value="true"/> 67 <param name="test" value="true"/>
68 </section> 68 </section>
69 <param name="in" value="IDRTCalibration_1_input.idXML"/> 69 <param name="in" value="IDRTCalibration_1_input.idXML"/>
70 <output name="out" file="IDRTCalibration_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 70 <output name="out" value="IDRTCalibration_1_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
71 <param name="calibrant_1_reference" value="0.1"/> 71 <param name="calibrant_1_reference" value="0.1"/>
72 <param name="calibrant_2_reference" value="0.9"/> 72 <param name="calibrant_2_reference" value="0.9"/>
73 <param name="calibrant_1_input" value="10.0"/> 73 <param name="calibrant_1_input" value="10.0"/>
74 <param name="calibrant_2_input" value="90.0"/> 74 <param name="calibrant_2_input" value="90.0"/>
75 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 75 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
76 <output name="ctd_out" ftype="xml"> 76 <output name="ctd_out" ftype="xml">
77 <assert_contents> 77 <assert_contents>
78 <is_valid_xml/> 78 <is_valid_xml/>
79 </assert_contents> 79 </assert_contents>
80 </output> 80 </output>
81 <assert_stdout>
82 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
83 </assert_stdout>
81 </test> 84 </test>
82 <!-- TOPP_IDRTCalibration_2 --> 85 <!-- TOPP_IDRTCalibration_2 -->
83 <test expect_num_outputs="2"> 86 <test expect_num_outputs="2">
84 <section name="adv_opts"> 87 <section name="adv_opts">
85 <param name="force" value="false"/> 88 <param name="force" value="false"/>
86 <param name="test" value="true"/> 89 <param name="test" value="true"/>
87 </section> 90 </section>
88 <param name="in" value="degenerated_empty.idXML"/> 91 <param name="in" value="degenerated_empty.idXML"/>
89 <output name="out" file="IDRTCalibration_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/> 92 <output name="out" value="IDRTCalibration_2_output.idXML" compare="sim_size" delta_frac="0.7" ftype="idxml"/>
90 <param name="calibrant_1_reference" value="0.1"/> 93 <param name="calibrant_1_reference" value="0.1"/>
91 <param name="calibrant_2_reference" value="0.9"/> 94 <param name="calibrant_2_reference" value="0.9"/>
92 <param name="calibrant_1_input" value="10.0"/> 95 <param name="calibrant_1_input" value="10.0"/>
93 <param name="calibrant_2_input" value="90.0"/> 96 <param name="calibrant_2_input" value="90.0"/>
94 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/> 97 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
95 <output name="ctd_out" ftype="xml"> 98 <output name="ctd_out" ftype="xml">
96 <assert_contents> 99 <assert_contents>
97 <is_valid_xml/> 100 <is_valid_xml/>
98 </assert_contents> 101 </assert_contents>
99 </output> 102 </output>
103 <assert_stdout>
104 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
105 </assert_stdout>
100 </test> 106 </test>
101 </tests> 107 </tests>
102 <help><![CDATA[Can be used to calibrate RTs of peptide hits linearly to standards. 108 <help><![CDATA[Can be used to calibrate RTs of peptide hits linearly to standards.
103 109
104 110
105 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRTCalibration.html]]></help> 111 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDRTCalibration.html]]></help>
106 <expand macro="references"/> 112 <expand macro="references"/>
107 </tool> 113 </tool>