Mercurial > repos > galaxyp > openms_mapnormalizer

comparison MapNormalizer.xml @ 13:c5ec10754228 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author galaxyp
date Thu, 27 Aug 2020 22:49:14 +0000
parents ef9eedba6d19
children 601713a1af9c
comparison
equal deleted inserted replaced
12:ef9eedba6d19 13:c5ec10754228
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: [Signal processing and preprocessing]--> 3 <!--Proposed Tool Section: [Signal processing and preprocessing]-->
4 <tool id="MapNormalizer" name="MapNormalizer" version="2.3.0"> 4 <tool id="MapNormalizer" name="MapNormalizer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Normalizes peak intensities in an MS run.</description> 5 <description>Normalizes peak intensities in an MS run.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">MapNormalizer</token> 7 <token name="@EXECUTABLE@">MapNormalizer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[MapNormalizer 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_in: 18 ## Preprocessing
16 -in $param_in 19 mkdir in &&
17 #end if 20 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
18 #if $param_out: 21 mkdir out &&
19 -out $param_out 22
20 #end if 23 ## Main program call
21 #if $adv_opts.adv_opts_selector=='advanced': 24
22 #if $adv_opts.param_force: 25 set -o pipefail &&
23 -force 26 @EXECUTABLE@ -write_ctd ./ &&
24 #end if 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 #end if 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 ]]></command> 29 -in
30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
31 -out
32 'out/output.${gxy2omsext("mzml")}'
33
34 ## Postprocessing
35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
38 #end if]]></command>
39 <configfiles>
40 <inputs name="args_json" data_style="paths"/>
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
42 </configfiles>
27 <inputs> 43 <inputs>
28 <param name="param_in" type="data" format="mzml" optional="False" label="input file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/>
29 <expand macro="advanced_options"> 45 <expand macro="adv_opts_macro">
30 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 46 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
47 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
48 <expand macro="list_string_san"/>
49 </param>
31 </expand> 50 </expand>
51 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
52 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
53 </param>
32 </inputs> 54 </inputs>
33 <outputs> 55 <outputs>
34 <data name="param_out" format="mzml"/> 56 <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">
58 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
59 </data>
35 </outputs> 60 </outputs>
36 <help>Normalizes peak intensities in an MS run. 61 <tests>
62 <expand macro="autotest_MapNormalizer"/>
63 <expand macro="manutest_MapNormalizer"/>
64 </tests>
65 <help><![CDATA[Normalizes peak intensities in an MS run.
37 66
38 67
39 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_MapNormalizer.html</help> 68 For more information, visit http://www.openms.de/documentation/TOPP_MapNormalizer.html]]></help>
69 <expand macro="references"/>
40 </tool> 70 </tool>