Mercurial > repos > galaxyp > openms_openswathchromatogramextractor

annotate OpenSwathChromatogramExtractor.xml @ 11:71555764c24a draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:01:42 +0000
parents e9c148b32f87
children f78d734b7c01
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--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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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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4 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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5 <description>Extract chromatograms (XIC) from a MS2 map file.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">OpenSwathChromatogramExtractor</token>
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8 <import>macros.xml</import>
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9 <import>macros_autotest.xml</import>
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10 <import>macros_test.xml</import>
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11 </macros>
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12 <expand macro="requirements"/>
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13 <expand macro="stdio"/>
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14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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15 @EXT_FOO@
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16 #import re
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17
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18 ## Preprocessing
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19 mkdir in &&
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20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) }
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21 mkdir tr &&
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22 ln -s '$tr' 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)' &&
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23 #if $rt_norm:
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24 mkdir rt_norm &&
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25 ln -s '$rt_norm' 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)' &&
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26 #end if
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27 mkdir out &&
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29 ## Main program call
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31 set -o pipefail &&
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32 @EXECUTABLE@ -write_ctd ./ &&
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33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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35 -in
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36 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])}
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37 -tr
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38 'tr/${re.sub("[^\w\-_]", "_", $tr.element_identifier)}.$gxy2omsext($tr.ext)'
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39 #if $rt_norm:
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40 -rt_norm
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41 'rt_norm/${re.sub("[^\w\-_]", "_", $rt_norm.element_identifier)}.$gxy2omsext($rt_norm.ext)'
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42 #end if
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43 -out
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44 'out/output.${gxy2omsext("mzml")}'
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45
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46 ## Postprocessing
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47 && mv 'out/output.${gxy2omsext("mzml")}' '$out'
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48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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50 #end if]]></command>
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51 <configfiles>
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52 <inputs name="args_json" data_style="paths"/>
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53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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54 </configfiles>
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55 <inputs>
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56 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input files separated by blank" help=" select mzml data sets(s)"/>
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57 <param name="tr" argument="-tr" type="data" format="csv,traml" optional="false" label="transition file ('TraML' or 'csv')" help=" select csv,traml data sets(s)"/>
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58 <param name="rt_norm" argument="-rt_norm" type="data" format="trafoxml" optional="true" label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" help=" select trafoxml data sets(s)"/>
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59 <param name="min_upper_edge_dist" argument="-min_upper_edge_dist" type="float" optional="true" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help=""/>
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60 <param name="rt_window" argument="-rt_window" type="float" optional="true" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range)" help="This is the full window size, e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
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61 <param name="ion_mobility_window" argument="-ion_mobility_window" type="float" optional="true" value="-1.0" label="Extraction window in ion mobility dimension (in milliseconds)" help="This is the full window size, e.g. a value of 10 milliseconds would extract 5 milliseconds on either side"/>
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62 <param name="mz_window" argument="-mz_window" type="float" optional="true" min="0.0" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag)" help="This is the full window size, e.g. 100 ppm would extract 50 ppm on either side"/>
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63 <param name="ppm" argument="-ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="m/z extraction_window is in ppm" help=""/>
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64 <param name="is_swath" argument="-is_swath" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Set this flag if the data is SWATH data" help=""/>
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65 <param name="extract_MS1" argument="-extract_MS1" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Extract the MS1 transitions based on the precursor values in the TraML file (useful for extracting MS1 XIC)" help=""/>
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66 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
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67 <param name="type" argument="-model:type" display="radio" type="select" optional="false" label="Type of model" help="">
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68 <option value="linear" selected="true">linear</option>
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69 <option value="b_spline">b_spline</option>
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70 <option value="interpolated">interpolated</option>
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71 <option value="lowess">lowess</option>
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72 <expand macro="list_string_san"/>
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73 </param>
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74 <param name="symmetric_regression" argument="-model:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
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75 </section>
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76 <expand macro="adv_opts_macro">
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77 <param name="extraction_function" argument="-extraction_function" display="radio" type="select" optional="false" label="Function used to extract the signal" help="">
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78 <option value="tophat" selected="true">tophat</option>
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79 <option value="bartlett">bartlett</option>
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80 <expand macro="list_string_san"/>
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81 </param>
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82 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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83 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
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84 <expand macro="list_string_san"/>
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85 </param>
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86 </expand>
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87 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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88 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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89 </param>
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90 </inputs>
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91 <outputs>
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92 <data name="out" label="${tool.name} on ${on_string}: out" format="mzml"/>
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93 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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94 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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95 </data>
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96 </outputs>
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97 <tests>
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98 <expand macro="autotest_OpenSwathChromatogramExtractor"/>
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99 <expand macro="manutest_OpenSwathChromatogramExtractor"/>
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100 </tests>
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101 <help><![CDATA[Extract chromatograms (XIC) from a MS2 map file.
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102
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103
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104 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_OpenSwathChromatogramExtractor.html]]></help>
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105 <expand macro="references"/>
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106 </tool>