Mercurial > repos > galaxyp > openms_spectrafilternormalizer

comparison SpectraFilterNormalizer.xml @ 9:8904d228594a 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, 03 Sep 2020 16:24:06 +0000
parents d82bd07d8190
children d736764156d9
comparison
equal deleted inserted replaced
8:77fd678d74f2 9:8904d228594a
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: [Identification]--> 3 <!--Proposed Tool Section: [Identification]-->
4 <tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="2.3.0"> 4 <tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Normalizes intensity of peak spectra.</description> 5 <description>Normalizes intensity of peak spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">SpectraFilterNormalizer</token> 7 <token name="@EXECUTABLE@">SpectraFilterNormalizer</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[SpectraFilterNormalizer 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 $param_algorithm_method: 24
22 -algorithm:method 25 set -o pipefail &&
23 #if " " in str($param_algorithm_method): 26 @EXECUTABLE@ -write_ctd ./ &&
24 "$param_algorithm_method" 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 #else 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 $param_algorithm_method 29 -in
27 #end if 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #end if 31 -out
29 #if $adv_opts.adv_opts_selector=='advanced': 32 'out/output.${gxy2omsext("mzml")}'
30 #if $adv_opts.param_force: 33
31 -force 34 ## Postprocessing
32 #end if 35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
33 #end if 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 ]]></command> 37 && mv '@EXECUTABLE@.ctd' '$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>
35 <inputs> 43 <inputs>
36 <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)"/>
37 <param name="param_algorithm_method" display="radio" type="select" optional="False" value="to_one" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="(-method) intensity of one ('to_one') per spectrum"> 45 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false">
38 <option value="to_one" selected="true">to_one</option> 46 <param name="method" argument="-algorithm:method" display="radio" type="select" optional="false" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum">
39 <option value="to_TIC">to_TIC</option> 47 <option value="to_one" selected="true">to_one</option>
48 <option value="to_TIC">to_TIC</option>
49 <expand macro="list_string_san"/>
50 </param>
51 </section>
52 <expand macro="adv_opts_macro">
53 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
54 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
55 <expand macro="list_string_san"/>
56 </param>
57 </expand>
58 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
40 </param> 60 </param>
41 <expand macro="advanced_options">
42 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
43 </expand>
44 </inputs> 61 </inputs>
45 <outputs> 62 <outputs>
46 <data name="param_out" format="mzml"/> 63 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
66 </data>
47 </outputs> 67 </outputs>
48 <help>Normalizes intensity of peak spectra. 68 <tests>
69 <expand macro="autotest_SpectraFilterNormalizer"/>
70 <expand macro="manutest_SpectraFilterNormalizer"/>
71 </tests>
72 <help><![CDATA[Normalizes intensity of peak spectra.
49 73
50 74
51 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_SpectraFilterNormalizer.html</help> 75 For more information, visit http://www.openms.de/documentation/TOPP_SpectraFilterNormalizer.html]]></help>
76 <expand macro="references"/>
52 </tool> 77 </tool>