Mercurial > repos > galaxyp > openms_noisefiltersgolay

comparison NoiseFilterSGolay.xml @ 13:7cd79c369f8d 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 23:17:54 +0000
parents cd0e5d7a8231
children b3133f5ee3fb
comparison
equal deleted inserted replaced
12:cd0e5d7a8231 13:7cd79c369f8d
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="NoiseFilterSGolay" name="NoiseFilterSGolay" version="2.3.0"> 4 <tool id="NoiseFilterSGolay" name="NoiseFilterSGolay" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description> 5 <description>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">NoiseFilterSGolay</token> 7 <token name="@EXECUTABLE@">NoiseFilterSGolay</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[NoiseFilterSGolay 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_frame_length: 24
22 -algorithm:frame_length $param_algorithm_frame_length 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_algorithm_polynomial_order: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -algorithm:polynomial_order $param_algorithm_polynomial_order 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #end if 29 -in
27 #if $adv_opts.adv_opts_selector=='advanced': 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 #if $adv_opts.param_processOption: 31 -out
29 -processOption 32 'out/output.${gxy2omsext("mzml")}'
30 #if " " in str($adv_opts.param_processOption): 33
31 "$adv_opts.param_processOption" 34 ## Postprocessing
32 #else 35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
33 $adv_opts.param_processOption 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #end if 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 #end if 38 #end if]]></command>
36 #if $adv_opts.param_force: 39 <configfiles>
37 -force 40 <inputs name="args_json" data_style="paths"/>
38 #end if 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 #end if 42 </configfiles>
40 ]]></command>
41 <inputs> 43 <inputs>
42 <param name="param_in" type="data" format="mzml" optional="False" label="input raw data file" help="(-in) "/> 44 <param name="in" argument="-in" type="data" format="mzml" optional="false" label="input raw data file" help=" select mzml data sets(s)"/>
43 <param name="param_algorithm_frame_length" type="integer" value="11" label="The number of subsequent data points used for smoothing" help="(-frame_length) &lt;br&gt;This number has to be uneven. If it is not, 1 will be added"/> 45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
44 <param name="param_algorithm_polynomial_order" type="integer" value="4" label="Order or the polynomial that is fitted" help="(-polynomial_order) "/> 46 <param name="frame_length" argument="-algorithm:frame_length" type="integer" optional="true" value="11" label="The number of subsequent data points used for smoothing" help="This number has to be uneven. If it is not, 1 will be added"/>
45 <expand macro="advanced_options"> 47 <param name="polynomial_order" argument="-algorithm:polynomial_order" type="integer" optional="true" value="4" label="Order or the polynomial that is fitted" help=""/>
46 <param name="param_processOption" display="radio" type="select" optional="False" value="inmemory" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="(-processOption) "> 48 </section>
49 <expand macro="adv_opts_macro">
50 <param name="processOption" argument="-processOption" display="radio" type="select" optional="false" label="Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first" help="">
47 <option value="inmemory" selected="true">inmemory</option> 51 <option value="inmemory" selected="true">inmemory</option>
48 <option value="lowmemory">lowmemory</option> 52 <option value="lowmemory">lowmemory</option>
53 <expand macro="list_string_san"/>
49 </param> 54 </param>
50 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 55 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
56 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
57 <expand macro="list_string_san"/>
58 </param>
51 </expand> 59 </expand>
60 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
61 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
62 </param>
52 </inputs> 63 </inputs>
53 <outputs> 64 <outputs>
54 <data name="param_out" format="mzml"/> 65 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
66 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
67 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
68 </data>
55 </outputs> 69 </outputs>
56 <help>Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data. 70 <tests>
71 <expand macro="autotest_NoiseFilterSGolay"/>
72 <expand macro="manutest_NoiseFilterSGolay"/>
73 </tests>
74 <help><![CDATA[Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
57 75
58 76
59 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_NoiseFilterSGolay.html</help> 77 For more information, visit http://www.openms.de/documentation/TOPP_NoiseFilterSGolay.html]]></help>
78 <expand macro="references"/>
60 </tool> 79 </tool>