Mercurial > repos > galaxyp > openms_rnpxlxicfilter

comparison RNPxlXICFilter.xml @ 12:81d5ef72ef9d 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 19:24:09 +0000
parents c2827f0ca312
children 8ee87d58ed48
comparison
equal deleted inserted replaced
11:beadd01e222c 12:81d5ef72ef9d
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="RNPxlXICFilter" name="RNPxlXICFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description> 5 <description>Remove MS2 spectra from treatment based on the fold change between control and treatment.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">RNPxlXICFilter</token> 7 <token name="@EXECUTABLE@">RNPxlXICFilter</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@
43 <configfiles> 41 <configfiles>
44 <inputs name="args_json" data_style="paths"/> 42 <inputs name="args_json" data_style="paths"/>
45 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 43 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
46 </configfiles> 44 </configfiles>
47 <inputs> 45 <inputs>
48 <param name="control" argument="-control" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/> 46 <param argument="-control" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/>
49 <param name="treatment" argument="-treatment" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/> 47 <param argument="-treatment" type="data" format="mzml" optional="false" label="input mzML file" help=" select mzml data sets(s)"/>
50 <param name="fold_change" argument="-fold_change" type="float" optional="true" value="2.0" label="fold change between XICs" help=""/> 48 <param argument="-fold_change" type="float" optional="true" value="2.0" label="fold change between XICs" help=""/>
51 <param name="rt_tol" argument="-rt_tol" type="float" optional="true" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/> 49 <param argument="-rt_tol" type="float" optional="true" value="20.0" label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" help=""/>
52 <param name="mz_tol" argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/> 50 <param argument="-mz_tol" type="float" optional="true" value="10.0" label="m/z tolerance in [ppm] for finding a peak" help=""/>
53 <expand macro="adv_opts_macro"> 51 <expand macro="adv_opts_macro">
54 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 52 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
55 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 53 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
56 <expand macro="list_string_san"/> 54 <expand macro="list_string_san" name="test"/>
57 </param> 55 </param>
58 </expand> 56 </expand>
59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 57 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 58 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
61 </param> 59 </param>
64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 62 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 63 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
66 <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>
67 </data> 65 </data>
68 </outputs> 66 </outputs>
69 <tests> 67 <tests><test expect_num_outputs="1"><!-- just chosen an arbitrary input (2x the same which is likely nonsense, but sufficient for the test) and autgenerated output-->
70 <expand macro="autotest_RNPxlXICFilter"/> 68 <param name="adv_opts|test" value="true"/>
71 <expand macro="manutest_RNPxlXICFilter"/> 69 <param name="control" ftype="mzml" value="FileFilter_1_input.mzML"/>
72 </tests> 70 <param name="treatment" ftype="mzml" value="FileFilter_1_input.mzML"/>
71 <output name="out" ftype="mzml" value="RNPxlXICFilter.mzML"/>
72 </test>
73 </tests>
73 <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment. 74 <help><![CDATA[Remove MS2 spectra from treatment based on the fold change between control and treatment.
74 75
75 76
76 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_RNPxlXICFilter.html]]></help> 77 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_RNPxlXICFilter.html]]></help>
77 <expand macro="references"/> 78 <expand macro="references"/>
78 </tool> 79 </tool>