Mercurial > repos > galaxyp > openms_baselinefilter

annotate BaselineFilter.xml @ 18:84bd73e60367 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 21:37:37 +0000
parents ddbae9eb797e
children
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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: peak smoothing / normalization]-->
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3 <tool id="BaselineFilter" name="BaselineFilter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Removes the baseline from profile spectra using a top-hat filter</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">BaselineFilter</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($in.ext)' &&
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18 mkdir out &&
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20 ## Main program call
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21
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22 set -o pipefail &&
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23 @EXECUTABLE@ -write_ctd ./ &&
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24 python3 '$__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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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 raw data file" help=" select mzml data sets(s)"/>
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42 <param argument="-struc_elem_length" type="float" value="3.0" label="Length of the structuring element (should be wider than maximal peak width - see documentation)" help=""/>
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43 <param argument="-struc_elem_unit" type="select" label="Unit of 'struc_elem_length' paramete" help="">
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44 <option value="Thomson" selected="true">Thomson</option>
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45 <option value="DataPoints">DataPoints</option>
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46 <expand macro="list_string_san" name="struc_elem_unit"/>
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47 </param>
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48 <param argument="-method" type="select" label="The name of the morphological filter to be applied" help="If you are unsure, use the default">
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49 <option value="identity">identity</option>
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50 <option value="erosion">erosion</option>
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51 <option value="dilation">dilation</option>
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52 <option value="opening">opening</option>
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53 <option value="closing">closing</option>
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54 <option value="gradient">gradient</option>
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55 <option value="tophat" selected="true">tophat</option>
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56 <option value="bothat">bothat</option>
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57 <option value="erosion_simple">erosion_simple</option>
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58 <option value="dilation_simple">dilation_simple</option>
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59 <expand macro="list_string_san" name="method"/>
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60 </param>
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61 <expand macro="adv_opts_macro">
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62 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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63 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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64 <expand macro="list_string_san" name="test"/>
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65 </param>
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66 </expand>
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67 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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68 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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69 </param>
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70 </inputs>
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71 <outputs>
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72 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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73 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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74 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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75 </data>
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76 </outputs>
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77 <tests>
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78 <!-- TOPP_BaselineFilter_1 -->
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79 <test expect_num_outputs="2">
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80 <section name="adv_opts">
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81 <param name="force" value="false"/>
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82 <param name="test" value="true"/>
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83 </section>
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84 <param name="in" value="BaselineFilter_input.mzML"/>
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85 <output name="out" value="BaselineFilter_output.mzML" compare="sim_size" delta_frac="0.7" ftype="mzml"/>
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86 <param name="struc_elem_length" value="1.5"/>
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87 <param name="struc_elem_unit" value="Thomson"/>
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88 <param name="method" value="tophat"/>
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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 </tests>
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100 <help><![CDATA[Removes the baseline from profile spectra using a top-hat filter.
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101
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102
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103 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_BaselineFilter.html]]></help>
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104 <expand macro="references"/>
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105 </tool>