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comparison MapStatistics.xml @ 14:905a2b83fa9d 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 21:33:50 +0000
parents 045995dc36bc
children
comparison
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13:045995dc36bc 14:905a2b83fa9d
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: [File Handling]--> 2 <!--Proposed Tool Section: [File Filtering / Extraction / Merging]-->
4 <tool id="MapStatistics" name="MapStatistics" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <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> 4 <description>Extract extended statistics on the features of a map for quality control</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">MapStatistics</token> 6 <token name="@EXECUTABLE@">MapStatistics</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="consensusxml,featurexml" optional="false" label="Input file" help=" select consensusxml,featurexml data sets(s)"/> 41 <param argument="-in" type="data" format="consensusxml,featurexml" label="Input file" help=" select consensusxml,featurexml data sets(s)"/>
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=""/> 42 <param argument="-n" type="integer" min="1" max="100" value="4" label="Report separate statistics for each of n RT slices of the map" help=""/>
44 <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/> 43 <param argument="-m" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show meta information about the whole experiment" help=""/>
45 <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/> 44 <param argument="-p" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Shows data processing information" help=""/>
46 <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a summary statistics of intensities, qualities, and widths" help=""/> 45 <param argument="-s" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Computes a summary statistics of intensities, qualities, and widths" help=""/>
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 ${on_string}: out" format="txt"/> 57 <data name="out" label="${tool.name} on ${on_string}: out" format="txt"/>
59 <data name="ctd_out" format="xml" label="${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><test expect_num_outputs="1"><!-- test with a featureXML input --> 62 <tests>
64 <param name="adv_opts|test" value="true"/> 63 <test expect_num_outputs="1">
65 <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/> 64 <!-- test with a featureXML input -->
66 <output name="out" ftype="txt" value="MapStatistics.txt"/> 65 <param name="adv_opts|test" value="true"/>
67 </test> 66 <param name="in" ftype="featurexml" value="SiriusAdapter_3_input.featureXML"/>
68 <test expect_num_outputs="1"><!-- test with a consensusxml input --> 67 <output name="out" ftype="txt" value="MapStatistics.txt"/>
69 <param name="adv_opts|test" value="true"/> 68 </test>
70 <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/> 69 <test expect_num_outputs="1">
71 <output name="out" ftype="txt" value="MapStatistics2.txt"/> 70 <!-- test with a consensusxml input -->
72 </test> 71 <param name="adv_opts|test" value="true"/>
73 </tests> 72 <param name="in" ftype="consensusxml" value="ConsensusXMLFile_1.consensusXML"/>
73 <output name="out" ftype="txt" value="MapStatistics2.txt"/>
74 </test>
75 </tests>
74 <help><![CDATA[Extract extended statistics on the features of a map for quality control. 76 <help><![CDATA[Extract extended statistics on the features of a map for quality control.
75 77
76 78
77 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_MapStatistics.html]]></help> 79 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapStatistics.html]]></help>
78 <expand macro="references"/> 80 <expand macro="references"/>
79 </tool> 81 </tool>