Mercurial > repos > galaxyp > openms_spectrafilterparentpeakmower

comparison SpectraFilterParentPeakMower.xml @ 14:2199afa87e7d draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:30:08 +0000
parents 5694ec584f4c
children
comparison
equal deleted inserted replaced
13:5694ec584f4c 14:2199afa87e7d
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="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> 3 <tool id="SpectraFilterParentPeakMower" name="SpectraFilterParentPeakMower" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Applies thresholdfilter to peak spectra.</description> 4 <description>Applies thresholdfilter to peak spectra</description>
6 <macros> 5 <macros>
7 <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</token> 6 <token name="@EXECUTABLE@">SpectraFilterParentPeakMower</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="window_size" argument="-algorithm:window_size" type="float" optional="true" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/> 43 <param name="window_size" argument="-algorithm:window_size" type="float" value="2.0" label="The size of the m/z window where the peaks are removed, +/- window_size" help=""/>
45 <param name="default_charge" argument="-algorithm:default_charge" type="integer" optional="true" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/> 44 <param name="default_charge" argument="-algorithm:default_charge" type="integer" value="2" label="If the precursor has no charge set, the default charge is assumed" help=""/>
46 <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" optional="true" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/> 45 <param name="clean_all_charge_states" argument="-algorithm:clean_all_charge_states" type="integer" value="1" label="Set to 1 if precursor ions of all possible charge states should be removed" help=""/>
47 <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" optional="true" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/> 46 <param name="consider_NH3_loss" argument="-algorithm:consider_NH3_loss" type="integer" value="1" label="Whether NH3 loss peaks from the precursor should be removed" help=""/>
48 <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" optional="true" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/> 47 <param name="consider_H2O_loss" argument="-algorithm:consider_H2O_loss" type="integer" value="1" label="Whether H2O loss peaks from the precursor should be removed" help=""/>
49 <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" optional="true" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/> 48 <param name="reduce_by_factor" argument="-algorithm:reduce_by_factor" type="integer" value="0" label="Reduce the intensities of the precursor and related ions by a given factor (set 'set_to_zero' to 0)" help=""/>
50 <param name="factor" argument="-algorithm:factor" type="float" optional="true" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/> 49 <param name="factor" argument="-algorithm:factor" type="float" value="1000.0" label="Factor which is used to reduce the intensities if 'reduce_by_factor' is selected" help=""/>
51 <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" optional="true" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/> 50 <param name="set_to_zero" argument="-algorithm:set_to_zero" type="integer" value="1" label="Reduce the intensities of the precursor and related ions to zero" help=""/>
52 </section> 51 </section>
53 <expand macro="adv_opts_macro"> 52 <expand macro="adv_opts_macro">
54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 53 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
55 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 54 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
56 <expand macro="list_string_san" name="test"/> 55 <expand macro="list_string_san" name="test"/>
57 </param> 56 </param>
58 </expand> 57 </expand>
59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 58 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 59 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/> 63 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 64 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 65 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
67 </data> 66 </data>
68 </outputs> 67 </outputs>
69 <tests><test expect_num_outputs="1"><!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output --> 68 <tests>
70 <param name="adv_opts|test" value="true"/> 69 <test expect_num_outputs="1">
71 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/> 70 <!-- copy pasted from autotest_SpectraFilterWindowMower (1st test) and autogenrated output -->
72 <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/> 71 <param name="adv_opts|test" value="true"/>
73 </test> 72 <param name="in" value="SpectraFilterSqrtMower_1_input.mzML"/>
74 </tests> 73 <output name="out" value="SpectraFilterParentPeakMower.mzML" compare="sim_size"/>
74 </test>
75 </tests>
75 <help><![CDATA[Applies thresholdfilter to peak spectra. 76 <help><![CDATA[Applies thresholdfilter to peak spectra.
76 77
77 78
78 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help> 79 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraFilterParentPeakMower.html]]></help>
79 <expand macro="references"/> 80 <expand macro="references"/>
80 </tool> 81 </tool>