Mercurial > repos > galaxyp > openms_peakpickeriterative

comparison PeakPickerIterative.xml @ 9:4bb4e2db2e77 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 19:46:58 -0400
parents eab30c6f4d08
children 0c37d0660a6b
comparison
equal deleted inserted replaced
8:d1fa2311a976 9:4bb4e2db2e77
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="PeakPickerIterative" name="PeakPickerIterative" version="2.3.0"> 4 <tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Finds mass spectrometric peaks in profile mass spectra.</description> 5 <description>Finds mass spectrometric peaks in profile mass spectra.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">PeakPickerIterative</token> 7 <token name="@EXECUTABLE@">PeakPickerIterative</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[PeakPickerIterative 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_signal_to_noise_: 24
22 -algorithm:signal_to_noise_ $param_algorithm_signal_to_noise_ 25 set -o pipefail &&
23 #end if 26 @EXECUTABLE@ -write_ctd ./ &&
24 #if $param_algorithm_peak_width: 27 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
25 -algorithm:peak_width $param_algorithm_peak_width 28 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
26 #end if 29 -in
27 #if $param_algorithm_ms1_only: 30 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
28 -algorithm:ms1_only 31 -out
29 #end if 32 'out/output.${gxy2omsext("mzml")}'
30 #if $param_algorithm_clear_meta_data: 33
31 -algorithm:clear_meta_data 34 ## Postprocessing
32 #end if 35 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
33 #if $adv_opts.adv_opts_selector=='advanced': 36 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
34 #if $adv_opts.param_force: 37 && mv '@EXECUTABLE@.ctd' '$ctd_out'
35 -force 38 #end if]]></command>
36 #end if 39 <configfiles>
37 #if $adv_opts.param_algorithm_spacing_difference: 40 <inputs name="args_json" data_style="paths"/>
38 -algorithm:spacing_difference $adv_opts.param_algorithm_spacing_difference 41 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
39 #end if 42 </configfiles>
40 #if $adv_opts.param_algorithm_sn_bin_count_:
41 -algorithm:sn_bin_count_ $adv_opts.param_algorithm_sn_bin_count_
42 #end if
43 #if $adv_opts.param_algorithm_nr_iterations_:
44 -algorithm:nr_iterations_ $adv_opts.param_algorithm_nr_iterations_
45 #end if
46 #if $adv_opts.param_algorithm_sn_win_len_:
47 -algorithm:sn_win_len_ $adv_opts.param_algorithm_sn_win_len_
48 #end if
49 #if $adv_opts.param_algorithm_check_width_internally:
50 -algorithm:check_width_internally
51 #end if
52 #end if
53 ]]></command>
54 <inputs> 43 <inputs>
55 <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)"/>
56 <param name="param_algorithm_signal_to_noise_" type="float" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help="(-signal_to_noise_) "/> 45 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
57 <param name="param_algorithm_peak_width" type="float" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="(-peak_width) In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/> 46 <param name="signal_to_noise_" argument="-algorithm:signal_to_noise_" type="float" optional="true" value="1.0" label="Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)" help=""/>
58 <param name="param_algorithm_ms1_only" display="radio" type="boolean" truevalue="-algorithm:ms1_only" falsevalue="" checked="false" optional="True" label="Only do MS1" help="(-ms1_only) "/> 47 <param name="peak_width" argument="-algorithm:peak_width" type="float" optional="true" value="0.0" label="Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing)" help="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
59 <param name="param_algorithm_clear_meta_data" display="radio" type="boolean" truevalue="-algorithm:clear_meta_data" falsevalue="" checked="false" optional="True" label="Delete meta data about peak width" help="(-clear_meta_data) "/> 48 <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" optional="true" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/>
60 <expand macro="advanced_options"> 49 <param name="sn_bin_count_" argument="-algorithm:sn_bin_count_" type="integer" optional="true" value="30" label="Bin count for the Signal to Noise estimation" help=""/>
61 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 50 <param name="nr_iterations_" argument="-algorithm:nr_iterations_" type="integer" optional="true" min="1" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help=""/>
62 <param name="param_algorithm_spacing_difference" type="float" value="1.5" label="Difference between peaks in multiples of the minimal difference to continue" help="(-spacing_difference) The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak"/> 51 <param name="sn_win_len_" argument="-algorithm:sn_win_len_" type="float" optional="true" value="20.0" label="Window length for the Signal to Noise estimation" help=""/>
63 <param name="param_algorithm_sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation" help="(-sn_bin_count_) "/> 52 <param name="check_width_internally" argument="-algorithm:check_width_internally" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help=""/>
64 <param name="param_algorithm_nr_iterations_" type="integer" min="1" optional="True" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help="(-nr_iterations_) "/> 53 <param name="ms1_only" argument="-algorithm:ms1_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only do MS1" help=""/>
65 <param name="param_algorithm_sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation" help="(-sn_win_len_) "/> 54 <param name="clear_meta_data" argument="-algorithm:clear_meta_data" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Delete meta data about peak width" help=""/>
66 <param name="param_algorithm_check_width_internally" display="radio" type="boolean" truevalue="-algorithm:check_width_internally" falsevalue="" checked="false" optional="True" label="Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)" help="(-check_width_internally) "/> 55 </section>
56 <expand macro="adv_opts_macro">
57 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
58 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
59 <expand macro="list_string_san"/>
60 </param>
67 </expand> 61 </expand>
62 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
63 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
64 </param>
68 </inputs> 65 </inputs>
69 <outputs> 66 <outputs>
70 <data name="param_out" format="mzml"/> 67 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
68 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
69 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
70 </data>
71 </outputs> 71 </outputs>
72 <help>Finds mass spectrometric peaks in profile mass spectra. 72 <tests>
73 <expand macro="autotest_PeakPickerIterative"/>
74 <expand macro="manutest_PeakPickerIterative"/>
75 </tests>
76 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
73 77
74 78
75 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/UTILS_PeakPickerIterative.html</help> 79 For more information, visit http://www.openms.de/documentation/UTILS_PeakPickerIterative.html]]></help>
80 <expand macro="references"/>
76 </tool> 81 </tool>