Mercurial > repos > galaxyp > openms_peakpickeriterative
comparison PeakPickerIterative.xml @ 9:4bb4e2db2e77 draft
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit ddf41e8bda1ba065f5cdec98e93dee8165ffc1b9"
author | galaxyp |
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date | Thu, 27 Aug 2020 19:46:58 -0400 |
parents | eab30c6f4d08 |
children | 0c37d0660a6b |
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8:d1fa2311a976 | 9:4bb4e2db2e77 |
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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: [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> |