Mercurial > repos > galaxyp > openms_spectrafilternormalizer
comparison SpectraFilterNormalizer.xml @ 9:8904d228594a draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 03 Sep 2020 16:24:06 +0000 |
parents | d82bd07d8190 |
children | d736764156d9 |
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8:77fd678d74f2 | 9:8904d228594a |
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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> |