Mercurial > repos > galaxyp > openms_spectramerger

annotate SpectraMerger.xml @ 14:b20b1f195cf2 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 21:28:09 +0000
parents 4333c513b7a1
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5b8e882b9fdc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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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: Misc / Helpers]-->
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3 <tool id="SpectraMerger" name="SpectraMerger" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Merges spectra (each MS level separately), increasing S/N ratios</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">SpectraMerger</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 mzML file" help=" select mzml data sets(s)"/>
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42 <param argument="-merging_method" type="select" label="Method of merging which should be used" help="">
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43 <option value="average_gaussian" selected="true">average_gaussian</option>
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44 <option value="average_tophat">average_tophat</option>
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45 <option value="precursor_method">precursor_method</option>
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46 <option value="block_method">block_method</option>
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47 <expand macro="list_string_san" name="merging_method"/>
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48 </param>
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49 <section name="algorithm" title="Algorithm section for merging spectra" help="" expanded="false">
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50 <param name="mz_binning_width" argument="-algorithm:mz_binning_width" type="float" min="0.0" value="5.0" label="minimum m/z distance for two data points (profile data) or peaks (centroided data) to be considered distinct" help="Closer data points or peaks will be merged"/>
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51 <param name="mz_binning_width_unit" argument="-algorithm:mz_binning_width_unit" type="select" label="Unit in which the distance between two data points or peaks is given" help="">
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52 <option value="Da">Da</option>
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53 <option value="ppm" selected="true">ppm</option>
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54 <expand macro="list_string_san" name="mz_binning_width_unit"/>
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55 </param>
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56 <param name="sort_blocks" argument="-algorithm:sort_blocks" type="select" label="Sort blocks by &lt;?&gt; before merging them (useful for precursor order)" help="">
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57 <option value="RT_ascending" selected="true">RT_ascending</option>
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58 <option value="RT_descending">RT_descending</option>
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59 <expand macro="list_string_san" name="sort_blocks"/>
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60 </param>
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61 <section name="average_gaussian" title="" help="" expanded="false">
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62 <param name="spectrum_type" argument="-algorithm:average_gaussian:spectrum_type" type="select" label="Spectrum type of the MS level to be averaged" help="">
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63 <option value="profile">profile</option>
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64 <option value="centroid">centroid</option>
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65 <option value="automatic" selected="true">automatic</option>
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66 <expand macro="list_string_san" name="spectrum_type"/>
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67 </param>
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68 <param name="ms_level" argument="-algorithm:average_gaussian:ms_level" type="integer" min="0" value="1" label="If set to be 0, each MS level will be merged from 1 to max" help="Otherwise, average spectra of this level. All other spectra remain unchanged"/>
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69 <param name="rt_FWHM" argument="-algorithm:average_gaussian:rt_FWHM" type="float" min="0.0" max="100000000000.0" value="5.0" label="FWHM of Gauss curve in seconds to be averaged ove" help=""/>
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70 <param name="cutoff" argument="-algorithm:average_gaussian:cutoff" type="float" min="0.0" max="1.0" value="0.01" label="Intensity cutoff for Gaussian" help="The Gaussian RT profile decreases from 1 at its apex to 0 at infinity. Spectra for which the intensity of the Gaussian drops below the cutoff do not contribute to the average"/>
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71 <param name="precursor_mass_tol" argument="-algorithm:average_gaussian:precursor_mass_tol" type="float" min="0.0" value="0.0" label="PPM mass tolerance for precursor mass" help="If set, MSn (n&gt;2) spectra of precursor masses within the tolerance are averaged"/>
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72 <param name="precursor_max_charge" argument="-algorithm:average_gaussian:precursor_max_charge" type="integer" min="1" value="1" label="Possible maximum precursor ion charge" help="Effective only when average_gaussian:precursor_mass_tol option is active"/>
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73 </section>
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74 <section name="average_tophat" title="" help="" expanded="false">
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75 <param name="spectrum_type" argument="-algorithm:average_tophat:spectrum_type" type="select" label="Spectrum type of the MS level to be averaged" help="">
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76 <option value="profile">profile</option>
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77 <option value="centroid">centroid</option>
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78 <option value="automatic" selected="true">automatic</option>
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79 <expand macro="list_string_san" name="spectrum_type"/>
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80 </param>
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81 <param name="ms_level" argument="-algorithm:average_tophat:ms_level" type="integer" min="0" value="1" label="If set to be 0, each MS level will be merged from 1 to max" help="Otherwise, average spectra of this level. All other spectra remain unchanged"/>
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82 <param name="rt_range" argument="-algorithm:average_tophat:rt_range" type="float" min="0.0" max="100000000000.0" value="5.0" label="RT range to be averaged ove" help="i.e. +/-(RT range)/2 from each spectrum"/>
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83 <param name="rt_unit" argument="-algorithm:average_tophat:rt_unit" type="select" label="Unit for RT range" help="">
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84 <option value="scans" selected="true">scans</option>
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85 <option value="seconds">seconds</option>
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86 <expand macro="list_string_san" name="rt_unit"/>
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87 </param>
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88 </section>
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89 <section name="block_method" title="" help="" expanded="false">
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90 <param name="ms_levels" argument="-algorithm:block_method:ms_levels" type="text" value="1" label="Merge spectra of this level" help="All spectra with other MS levels remain untouched (space separated list, in order to allow for spaces in list items surround them by single quotes)">
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91 <expand macro="list_integer_valsan" name="ms_levels">
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92 <validator type="expression" message="a space separated list of integer values in the range 1: is required"><![CDATA[len(value.split(' ')) == len([_ for _ in value.split(' ') if 1 <= int(_)])
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93 ]]></validator>
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94 </expand>
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95 </param>
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96 <param name="rt_block_size" argument="-algorithm:block_method:rt_block_size" type="integer" min="1" value="5" label="Maximum number of scans to be summed up" help=""/>
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97 <param name="rt_max_length" argument="-algorithm:block_method:rt_max_length" type="float" min="0.0" max="100000000000.0" value="0.0" label="Maximum RT size of the block in seconds (0.0 = no size restriction)" help=""/>
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98 </section>
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99 <section name="precursor_method" title="" help="" expanded="false">
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100 <param name="mz_tolerance" argument="-algorithm:precursor_method:mz_tolerance" type="float" min="0.0" value="0.0001" label="Max m/z distance of the precursor entries of two spectra to be merged in [Da]" help=""/>
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101 <param name="mass_tolerance" argument="-algorithm:precursor_method:mass_tolerance" type="float" min="0.0" value="0.0" label="Max mass distance of the precursor entries of two spectra to be merged in [Da]" help="Active when set to a positive value"/>
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102 <param name="rt_tolerance" argument="-algorithm:precursor_method:rt_tolerance" type="float" min="0.0" value="5.0" label="Max RT distance of the precursor entries of two spectra to be merged in [s]" help=""/>
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103 </section>
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104 </section>
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105 <expand macro="adv_opts_macro">
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106 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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107 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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108 <expand macro="list_string_san" name="test"/>
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109 </param>
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110 </expand>
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111 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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112 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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113 </param>
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114 </inputs>
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115 <outputs>
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116 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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117 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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118 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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119 </data>
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120 </outputs>
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121 <tests>
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122 <test expect_num_outputs="1">
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123 <!-- just chosen an arbitrary input and autgenerated output-->
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124 <param name="adv_opts|test" value="true"/>
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125 <param name="in" ftype="mzml" value="NovorAdapter_in.mzML"/>
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126 <section name="algorithm">
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127 <section name="average_gaussian">
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128 <param name="ms_level" value="2"/>
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129 </section>
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130 </section>
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131 <output name="out" ftype="mzml" value="SpectraMerger_1.mzML" compare="sim_size"/>
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132 </test>
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133 </tests>
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134 <help><![CDATA[Merges spectra (each MS level separately), increasing S/N ratios.
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135
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136
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137 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_SpectraMerger.html]]></help>
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138 <expand macro="references"/>
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139 </tool>