Mercurial > repos > galaxyp > openms_idrtcalibration

comparison IDRTCalibration.xml @ 14:7ff821b34ebc draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:25:24 +0000
parents 28805cf9b024
children f7226e34dc70
comparison
equal deleted inserted replaced
13:c4e15b449974 14:7ff821b34ebc
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: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="IDRTCalibration" name="IDRTCalibration" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <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> 5 <description>Can be used to calibrate RTs of peptide hits linearly to standards.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDRTCalibration</token> 7 <token name="@EXECUTABLE@">IDRTCalibration</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@
39 <configfiles> 37 <configfiles>
40 <inputs name="args_json" data_style="paths"/> 38 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles> 40 </configfiles>
43 <inputs> 41 <inputs>
44 <param name="in" argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> 42 <param argument="-in" type="data" format="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/>
45 <param name="calibrant_1_reference" argument="-calibrant_1_reference" type="float" optional="true" value="0.1" label="The RT of the first calibrant in the reference file" help=""/> 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=""/>
46 <param name="calibrant_2_reference" argument="-calibrant_2_reference" type="float" optional="true" value="0.9" label="The RT of the second 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=""/>
47 <param name="calibrant_1_input" 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"/> 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"/>
48 <param name="calibrant_2_input" 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"/> 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"/>
49 <expand macro="adv_opts_macro"> 47 <expand macro="adv_opts_macro">
50 <param name="force" 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=""/>
51 <param name="test" 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" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
52 <expand macro="list_string_san"/> 50 <expand macro="list_string_san" name="test"/>
53 </param> 51 </param>
54 </expand> 52 </expand>
55 <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">
56 <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>
57 </param> 55 </param>
60 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 58 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
61 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 59 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
62 <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>
63 </data> 61 </data>
64 </outputs> 62 </outputs>
65 <tests> 63 <tests><!-- TOPP_IDRTCalibration_1 -->
66 <expand macro="autotest_IDRTCalibration"/> 64 <test expect_num_outputs="2">
67 <expand macro="manutest_IDRTCalibration"/> 65 <section name="adv_opts">
66 <param name="force" value="false"/>
67 <param name="test" value="true"/>
68 </section>
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"/>
71 <param name="calibrant_1_reference" value="0.1"/>
72 <param name="calibrant_2_reference" value="0.9"/>
73 <param name="calibrant_1_input" value="10.0"/>
74 <param name="calibrant_2_input" value="90.0"/>
75 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
76 <output name="ctd_out" ftype="xml">
77 <assert_contents>
78 <is_valid_xml/>
79 </assert_contents>
80 </output>
81 </test>
82 <!-- TOPP_IDRTCalibration_2 -->
83 <test expect_num_outputs="2">
84 <section name="adv_opts">
85 <param name="force" value="false"/>
86 <param name="test" value="true"/>
87 </section>
88 <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"/>
90 <param name="calibrant_1_reference" value="0.1"/>
91 <param name="calibrant_2_reference" value="0.9"/>
92 <param name="calibrant_1_input" value="10.0"/>
93 <param name="calibrant_2_input" value="90.0"/>
94 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
95 <output name="ctd_out" ftype="xml">
96 <assert_contents>
97 <is_valid_xml/>
98 </assert_contents>
99 </output>
100 </test>
68 </tests> 101 </tests>
69 <help><![CDATA[Can be used to calibrate RTs of peptide hits linearly to standards. 102 <help><![CDATA[Can be used to calibrate RTs of peptide hits linearly to standards.
70 103
71 104
72 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_IDRTCalibration.html]]></help> 105 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_IDRTCalibration.html]]></help>
73 <expand macro="references"/> 106 <expand macro="references"/>
74 </tool> 107 </tool>