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comparison IDExtractor.xml @ 16:a6124b08daff 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 21:28:53 +0000
parents 589bf635f424
children
comparison
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15:589bf635f424 16:a6124b08daff
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: [Utilities]--> 2 <!--Proposed Tool Section: [Identification Processing]-->
4 <tool id="IDExtractor" name="IDExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="IDExtractor" name="IDExtractor" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Extracts 'n' peptides randomly or best 'n' from idXML files.</description> 4 <description>Extracts 'n' peptides randomly or best 'n' from idXML files</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">IDExtractor</token> 6 <token name="@EXECUTABLE@">IDExtractor</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="idxml" optional="false" label="input file" help=" select idxml data sets(s)"/> 41 <param argument="-in" type="data" format="idxml" label="input file" help=" select idxml data sets(s)"/>
43 <param argument="-number_of_peptides" type="integer" optional="true" min="1" value="10" label="Number of randomly chosen peptides" help=""/> 42 <param argument="-number_of_peptides" type="integer" min="1" value="10" label="Number of randomly chosen peptides" help=""/>
44 <param argument="-number_of_rand_invokations" type="integer" optional="true" min="0" value="0" label="Number of rand invocations before random draw (basically a seed)" help=""/> 43 <param argument="-number_of_rand_invokations" type="integer" min="0" value="0" label="Number of rand invocations before random draw (basically a seed)" help=""/>
45 <param argument="-best_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the best n peptides are chosen" help=""/> 44 <param argument="-best_hits" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is set the best n peptides are chosen" help=""/>
46 <expand macro="adv_opts_macro"> 45 <expand macro="adv_opts_macro">
47 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 46 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
48 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 47 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
49 <expand macro="list_string_san" name="test"/> 48 <expand macro="list_string_san" name="test"/>
50 </param> 49 </param>
51 </expand> 50 </expand>
52 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 51 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
53 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 52 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
57 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/> 56 <data name="out" label="${tool.name} on ${on_string}: out" format="idxml"/>
58 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 57 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
59 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 58 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
60 </data> 59 </data>
61 </outputs> 60 </outputs>
62 <tests><test expect_num_outputs="1"><!-- --> 61 <tests>
63 <param name="adv_opts|test" value="true"/> 62 <test expect_num_outputs="1">
64 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/> 63 <!-- -->
65 <param name="best_hits" value="true"/> 64 <param name="adv_opts|test" value="true"/>
66 <param name="number_of_peptides" value="1"/> 65 <param name="in" ftype="idxml" value="MSGFPlusAdapter_1_out.idXML"/>
67 <output name="out" value="IDExtractor.idXML" compare="sim_size"/> 66 <param name="best_hits" value="true"/>
68 </test> 67 <param name="number_of_peptides" value="1"/>
69 </tests> 68 <output name="out" value="IDExtractor.idXML" compare="sim_size"/>
69 </test>
70 </tests>
70 <help><![CDATA[Extracts 'n' peptides randomly or best 'n' from idXML files. 71 <help><![CDATA[Extracts 'n' peptides randomly or best 'n' from idXML files.
71 72
72 73
73 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDExtractor.html]]></help> 74 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_IDExtractor.html]]></help>
74 <expand macro="references"/> 75 <expand macro="references"/>
75 </tool> 76 </tool>