Mercurial > repos > galaxyp > openms_spectrafilterthresholdmower

comparison SpectraFilterThresholdMower.xml @ 13:1db101600feb 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 18:58:49 +0000
parents dd4ae875c004
children 53fec73970ad
comparison
equal deleted inserted replaced
12:da2ece63688b 13:1db101600feb
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: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="SpectraFilterThresholdMower" name="SpectraFilterThresholdMower" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="SpectraFilterThresholdMower" name="SpectraFilterThresholdMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies thresholdfilter to peak spectra.</description> 5 <description>Applies thresholdfilter to peak spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SpectraFilterThresholdMower</token> 7 <token name="@EXECUTABLE@">SpectraFilterThresholdMower</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="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> 42 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
45 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false"> 43 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
46 <param name="threshold" argument="-algorithm:threshold" type="float" optional="true" value="0.05" label="Intensity threshold, peaks below this threshold are discarded" help=""/> 44 <param name="threshold" argument="-algorithm:threshold" type="float" optional="true" value="0.05" label="Intensity threshold, peaks below this threshold are discarded" help=""/>
47 </section> 45 </section>
48 <expand macro="adv_opts_macro"> 46 <expand macro="adv_opts_macro">
49 <param name="force" 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=""/>
50 <param name="test" 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" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
51 <expand macro="list_string_san"/> 49 <expand macro="list_string_san" name="test"/>
52 </param> 50 </param>
53 </expand> 51 </expand>
54 <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">
55 <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>
56 </param> 54 </param>
59 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 57 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
60 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
61 <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>
62 </data> 60 </data>
63 </outputs> 61 </outputs>
64 <tests> 62 <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
65 <expand macro="autotest_SpectraFilterThresholdMower"/> 63 <param name="adv_opts|test" value="true"/>
66 <expand macro="manutest_SpectraFilterThresholdMower"/> 64 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
67 </tests> 65 <output name="out" value="SpectraFilterThresholdMower.mzML" compare="sim_size"/>
66 </test>
67 </tests>
68 <help><![CDATA[Applies thresholdfilter to peak spectra. 68 <help><![CDATA[Applies thresholdfilter to peak spectra.
69 69
70 70
71 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpectraFilterThresholdMower.html]]></help> 71 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterThresholdMower.html]]></help>
72 <expand macro="references"/> 72 <expand macro="references"/>
73 </tool> 73 </tool>