Mercurial > repos > galaxyp > openms_demeanderize

comparison DeMeanderize.xml @ 18:17547aceaf40 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 21:38:10 +0000
parents 2425a98560f5
children
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17:2425a98560f5 18:17547aceaf40
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: [Misc / Helpers]-->
4 <tool id="DeMeanderize" name="DeMeanderize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="DeMeanderize" name="DeMeanderize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Orders the spectra of MALDI spotting plates correctly.</description> 4 <description>Orders the spectra of MALDI spotting plates correctly</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">DeMeanderize</token> 6 <token name="@EXECUTABLE@">DeMeanderize</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="mzml" optional="false" label="Input experiment file, containing the wrongly sorted spectra" help=" select mzml data sets(s)"/> 41 <param argument="-in" type="data" format="mzml" label="Input experiment file, containing the wrongly sorted spectra" help=" select mzml data sets(s)"/>
43 <param argument="-num_spots_per_row" type="integer" optional="true" min="1" value="48" label="Number of spots in one column, until next row is spotted" help=""/> 42 <param argument="-num_spots_per_row" type="integer" min="1" value="48" label="Number of spots in one column, until next row is spotted" help=""/>
44 <expand macro="adv_opts_macro"> 43 <expand macro="adv_opts_macro">
45 <param argument="-RT_distance" type="float" optional="true" min="0.0" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT" help=""/> 44 <param argument="-RT_distance" type="float" min="0.0" value="1.0" label="RT distance between two spots which is used to calculated pseudo RT" help=""/>
46 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 45 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
47 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 46 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
48 <expand macro="list_string_san" name="test"/> 47 <expand macro="list_string_san" name="test"/>
49 </param> 48 </param>
50 </expand> 49 </expand>
51 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 50 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
52 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 51 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
56 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 55 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
57 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 56 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
58 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 57 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
59 </data> 58 </data>
60 </outputs> 59 </outputs>
61 <tests><test expect_num_outputs="1"><!-- test with the output of a MSsimulator output generated by a test below --> 60 <tests/>
62 <param name="adv_opts|test" value="true"/>
63 <param name="in" ftype="mzml" value="MSsimulator_MALDI.mzml"/>
64 <output name="out" ftype="mzml" value="DeMeanderize.mzml"/>
65 </test>
66 </tests>
67 <help><![CDATA[Orders the spectra of MALDI spotting plates correctly. 61 <help><![CDATA[Orders the spectra of MALDI spotting plates correctly.
68 62
69 63
70 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_DeMeanderize.html]]></help> 64 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_DeMeanderize.html]]></help>
71 <expand macro="references"/> 65 <expand macro="references"/>
72 </tool> 66 </tool>