Mercurial > repos > galaxyp > openms_mapstatistics

comparison MapStatistics.xml @ 13:045995dc36bc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:16:16 +0000
parents 9e25560d4ded
children 905a2b83fa9d
comparison
equal deleted inserted replaced
12:9cdd5faa34d0 13:045995dc36bc
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: [File Handling]--> 3 <!--Proposed Tool Section: [File Handling]-->
4 <tool id="MapStatistics" name="MapStatistics" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="MapStatistics" name="MapStatistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Extract extended statistics on the features of a map for quality control.</description> 5 <description>Extract extended statistics on the features of a map for quality control.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MapStatistics</token> 7 <token name="@EXECUTABLE@">MapStatistics</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="consensusxml,featurexml" optional="false" label="Input file" help=" select consensusxml,featurexml data sets(s)"/> 42 <param argument="-in" type="data" format="consensusxml,featurexml" optional="false" label="Input file" help=" select consensusxml,featurexml data sets(s)"/>
45 <param name="n" argument="-n" type="integer" optional="true" min="1" max="100" value="4" label="Report separate statistics for each of n RT slices of the map" help=""/> 43 <param argument="-n" type="integer" optional="true" min="1" max="100" value="4" label="Report separate statistics for each of n RT slices of the map" help=""/>
46 <param name="m" argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/> 44 <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
47 <param name="p" argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/> 45 <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
48 <param name="s" argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a summary statistics of intensities, qualities, and widths" help=""/> 46 <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a summary statistics of intensities, qualities, and widths" help=""/>
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 ${on_string}: out" format="txt"/> 58 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
61 <data name="ctd_out" format="xml" label="${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><test expect_num_outputs="1"><!-- test with a featureXML input -->
66 <expand macro="autotest_MapStatistics"/> 64 <param name="adv_opts|test" value="true"/>
67 <expand macro="manutest_MapStatistics"/> 65 <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/>
68 </tests> 66 <output name="out" ftype="txt" value="MapStatistics.txt"/>
67 </test>
68 <test expect_num_outputs="1"><!-- test with a consensusxml input -->
69 <param name="adv_opts|test" value="true"/>
70 <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
71 <output name="out" ftype="txt" value="MapStatistics2.txt"/>
72 </test>
73 </tests>
69 <help><![CDATA[Extract extended statistics on the features of a map for quality control. 74 <help><![CDATA[Extract extended statistics on the features of a map for quality control.
70 75
71 76
72 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_MapStatistics.html]]></help> 77 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapStatistics.html]]></help>
73 <expand macro="references"/> 78 <expand macro="references"/>
74 </tool> 79 </tool>