Mercurial > repos > galaxyp > openms_spectrafilternormalizer
comparison SpectraFilterNormalizer.xml @ 13:e4f9ce9d90ad draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:10:52 +0000 |
parents | d736764156d9 |
children | 4ba7fb47318c |
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12:4dbf90919a9f | 13:e4f9ce9d90ad |
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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="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> | 4 <tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
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> | |
11 </macros> | 9 </macros> |
12 <expand macro="requirements"/> | 10 <expand macro="requirements"/> |
13 <expand macro="stdio"/> | 11 <expand macro="stdio"/> |
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ | 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ |
15 @EXT_FOO@ | 13 @EXT_FOO@ |
39 <configfiles> | 37 <configfiles> |
40 <inputs name="args_json" data_style="paths"/> | 38 <inputs name="args_json" data_style="paths"/> |
41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> | 39 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> |
42 </configfiles> | 40 </configfiles> |
43 <inputs> | 41 <inputs> |
44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> | 42 <param argument="-in" type="data" format="mzml" optional="false" label="input file" help=" select mzml data sets(s)"/> |
45 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false"> | 43 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false"> |
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"> | 44 <param name="method" argument="-algorithm:method" type="select" optional="true" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum"> |
47 <option value="to_one" selected="true">to_one</option> | 45 <option value="to_one" selected="true">to_one</option> |
48 <option value="to_TIC">to_TIC</option> | 46 <option value="to_TIC">to_TIC</option> |
49 <expand macro="list_string_san"/> | 47 <expand macro="list_string_san" name="method"/> |
50 </param> | 48 </param> |
51 </section> | 49 </section> |
52 <expand macro="adv_opts_macro"> | 50 <expand macro="adv_opts_macro"> |
53 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 51 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides 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=""> | 52 <param 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"/> | 53 <expand macro="list_string_san" name="test"/> |
56 </param> | 54 </param> |
57 </expand> | 55 </expand> |
58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 56 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 57 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
60 </param> | 58 </param> |
63 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> | 61 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
66 </data> | 64 </data> |
67 </outputs> | 65 </outputs> |
68 <tests> | 66 <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> |
69 <expand macro="autotest_SpectraFilterNormalizer"/> | 67 <param name="adv_opts|test" value="true"/> |
70 <expand macro="manutest_SpectraFilterNormalizer"/> | 68 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> |
71 </tests> | 69 <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/> |
70 </test> | |
71 </tests> | |
72 <help><![CDATA[Normalizes intensity of peak spectra. | 72 <help><![CDATA[Normalizes intensity of peak spectra. |
73 | 73 |
74 | 74 |
75 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_SpectraFilterNormalizer.html]]></help> | 75 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterNormalizer.html]]></help> |
76 <expand macro="references"/> | 76 <expand macro="references"/> |
77 </tool> | 77 </tool> |