Mercurial > repos > galaxyp > openms_spectrafilternormalizer
comparison SpectraFilterNormalizer.xml @ 14:4ba7fb47318c draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:30:31 +0000 |
parents | e4f9ce9d90ad |
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13:e4f9ce9d90ad | 14:4ba7fb47318c |
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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: [Identification]--> | 2 <!--Proposed Tool Section: [Spectrum processing: peak smoothing / normalization]--> |
4 <tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> | 3 <tool id="SpectraFilterNormalizer" name="SpectraFilterNormalizer" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> |
5 <description>Normalizes intensity of peak spectra.</description> | 4 <description>Normalizes intensity of peak spectra</description> |
6 <macros> | 5 <macros> |
7 <token name="@EXECUTABLE@">SpectraFilterNormalizer</token> | 6 <token name="@EXECUTABLE@">SpectraFilterNormalizer</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 file" help=" select mzml data sets(s)"/> | 41 <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/> |
43 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false"> | 42 <section name="algorithm" title="Algorithm parameter subsection" help="" expanded="false"> |
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"> | 43 <param name="method" argument="-algorithm:method" type="select" label="Normalize via dividing by TIC ('to_TIC') per spectrum or normalize to max" help="intensity of one ('to_one') per spectrum"> |
45 <option value="to_one" selected="true">to_one</option> | 44 <option value="to_one" selected="true">to_one</option> |
46 <option value="to_TIC">to_TIC</option> | 45 <option value="to_TIC">to_TIC</option> |
47 <expand macro="list_string_san" name="method"/> | 46 <expand macro="list_string_san" name="method"/> |
48 </param> | 47 </param> |
49 </section> | 48 </section> |
50 <expand macro="adv_opts_macro"> | 49 <expand macro="adv_opts_macro"> |
51 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> | 50 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> |
52 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> | 51 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true"> |
53 <expand macro="list_string_san" name="test"/> | 52 <expand macro="list_string_san" name="test"/> |
54 </param> | 53 </param> |
55 </expand> | 54 </expand> |
56 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> | 55 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> |
57 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> | 56 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> |
61 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> | 60 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> |
62 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> | 61 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> |
63 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> | 62 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> |
64 </data> | 63 </data> |
65 </outputs> | 64 </outputs> |
66 <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> | 65 <tests> |
67 <param name="adv_opts|test" value="true"/> | 66 <test expect_num_outputs="1"> |
68 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> | 67 <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> |
69 <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/> | 68 <param name="adv_opts|test" value="true"/> |
70 </test> | 69 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> |
71 </tests> | 70 <output name="out" value="SpectraFilterNormalizer.mzML" compare="sim_size"/> |
71 </test> | |
72 </tests> | |
72 <help><![CDATA[Normalizes intensity of peak spectra. | 73 <help><![CDATA[Normalizes intensity of peak spectra. |
73 | 74 |
74 | 75 |
75 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterNormalizer.html]]></help> | 76 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterNormalizer.html]]></help> |
76 <expand macro="references"/> | 77 <expand macro="references"/> |
77 </tool> | 78 </tool> |