Mercurial > repos > galaxyp > openms_peakpickeriterative

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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 21:32:08 +0000
parents 9547baeca6a1
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1 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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2 <!--Proposed Tool Section: [Spectrum processing: Centroiding]-->
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3 <tool id="PeakPickerIterative" name="PeakPickerIterative" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Finds mass spectrometric peaks in profile mass spectra</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">PeakPickerIterative</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 mkdir out &&
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20 ## Main program call
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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25 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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26 -in
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27 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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28 -out
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29 'out/output.${gxy2omsext("mzml")}'
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30
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31 ## Postprocessing
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32 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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33 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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34 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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35 #end if]]></command>
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36 <configfiles>
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37 <inputs name="args_json" data_style="paths"/>
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38 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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39 </configfiles>
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40 <inputs>
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41 <param argument="-in" type="data" format="mzml" label="input file" help=" select mzml data sets(s)"/>
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42 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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43 <param name="signal_to_noise_" argument="-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=""/>
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44 <param name="peak_width" argument="-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="In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value"/>
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45 <param name="spacing_difference" argument="-algorithm:spacing_difference" type="float" 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"/>
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46 <param name="sn_bin_count_" argument="-algorithm:sn_bin_count_" type="integer" value="30" label="Bin count for the Signal to Noise estimation" help=""/>
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47 <param name="nr_iterations_" argument="-algorithm:nr_iterations_" type="integer" min="1" value="5" label="Nr of iterations to perform (how many times the peaks are re-centered)" help=""/>
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48 <param name="sn_win_len_" argument="-algorithm:sn_win_len_" type="float" value="20.0" label="Window length for the Signal to Noise estimation" help=""/>
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49 <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=""/>
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50 <param name="ms1_only" argument="-algorithm:ms1_only" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only do MS1" help=""/>
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51 <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=""/>
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52 </section>
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53 <expand macro="adv_opts_macro">
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54 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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55 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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56 <expand macro="list_string_san" name="test"/>
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57 </param>
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58 </expand>
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59 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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60 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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61 </param>
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62 </inputs>
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63 <outputs>
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64 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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65 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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66 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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67 </data>
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68 </outputs>
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69 <tests>
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70 <!-- TOPP_PeakPickerIterative_1 -->
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71 <test expect_num_outputs="2">
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72 <section name="adv_opts">
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73 <param name="force" value="false"/>
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74 <param name="test" value="true"/>
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75 </section>
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76 <param name="in" value="PeakPickerIterative_1_input.mzML"/>
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77 <output name="out" value="PeakPickerIterative_1_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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78 <section name="algorithm">
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79 <param name="signal_to_noise_" value="1.0"/>
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80 <param name="peak_width" value="0.04"/>
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81 <param name="spacing_difference" value="1.5"/>
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82 <param name="sn_bin_count_" value="30"/>
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83 <param name="nr_iterations_" value="5"/>
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84 <param name="sn_win_len_" value="20.0"/>
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85 <param name="check_width_internally" value="false"/>
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86 <param name="ms1_only" value="false"/>
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87 <param name="clear_meta_data" value="false"/>
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88 </section>
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89 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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90 <output name="ctd_out" ftype="xml">
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91 <assert_contents>
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92 <is_valid_xml/>
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93 </assert_contents>
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94 </output>
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95 <assert_stdout>
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96 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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97 </assert_stdout>
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98 </test>
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99 <!-- TOPP_PeakPickerIterative_2 -->
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100 <test expect_num_outputs="2">
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101 <section name="adv_opts">
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102 <param name="force" value="false"/>
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103 <param name="test" value="true"/>
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104 </section>
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105 <param name="in" value="PeakPickerIterative_2_input.mzML"/>
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106 <output name="out" value="PeakPickerIterative_2_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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107 <section name="algorithm">
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108 <param name="signal_to_noise_" value="0.0"/>
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109 <param name="peak_width" value="0.04"/>
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110 <param name="spacing_difference" value="2.5"/>
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111 <param name="sn_bin_count_" value="30"/>
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112 <param name="nr_iterations_" value="5"/>
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113 <param name="sn_win_len_" value="20.0"/>
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114 <param name="check_width_internally" value="true"/>
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115 <param name="ms1_only" value="false"/>
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116 <param name="clear_meta_data" value="false"/>
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117 </section>
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118 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG"/>
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119 <output name="ctd_out" ftype="xml">
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120 <assert_contents>
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121 <is_valid_xml/>
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122 </assert_contents>
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123 </output>
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124 <assert_stdout>
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125 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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126 </assert_stdout>
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127 </test>
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128 </tests>
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129 <help><![CDATA[Finds mass spectrometric peaks in profile mass spectra.
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130
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131
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132 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_PeakPickerIterative.html]]></help>
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133 <expand macro="references"/>
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134 </tool>