Mercurial > repos > galaxyp > openms_openswathchromatogramextractor

annotate OpenSwathChromatogramExtractor.xml @ 3:a4e9284d9ecb draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit d4b74e94ddabaccec6b1c5f9540d074c39207600
author galaxyp
date Sat, 28 Oct 2017 05:21:15 -0400
parents 47729465a3d3
children ebe0e9442a29
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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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Targeted Experiments]-->
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4 <tool id="OpenSwathChromatogramExtractor" name="OpenSwathChromatogramExtractor" version="2.2.0">
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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 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>OpenSwathChromatogramExtractor
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14
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15 -in
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16 #for token in $param_in:
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17 $token
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18 #end for
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19 #if $param_tr:
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20 -tr $param_tr
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21 #end if
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22 #if $param_rt_norm:
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23 -rt_norm $param_rt_norm
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24 #end if
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25 #if $param_out:
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26 -out $param_out
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27 #end if
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28 #if $param_min_upper_edge_dist:
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29 -min_upper_edge_dist $param_min_upper_edge_dist
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30 #end if
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31 #if $param_mz_window:
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32 -mz_window $param_mz_window
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33 #end if
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34 #if $param_rt_window:
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35 -rt_window $param_rt_window
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36 #end if
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37 #if $param_is_swath:
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38 -is_swath
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39 #end if
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40 #if $param_ppm:
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41 -ppm
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42 #end if
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43 #if $param_extract_MS1:
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44 -extract_MS1
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45 #end if
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46 #if $param_extraction_function:
1
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47 -extraction_function
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48 #if " " in str($param_extraction_function):
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49 "$param_extraction_function"
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50 #else
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51 $param_extraction_function
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52 #end if
0
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53 #end if
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54 #if $param_model_type:
1
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55 -model:type
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56 #if " " in str($param_model_type):
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57 "$param_model_type"
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58 #else
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59 $param_model_type
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60 #end if
0
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61 #end if
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62 #if $param_model_symmetric_regression:
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63 -model:symmetric_regression
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64 #end if
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65 #if $adv_opts.adv_opts_selector=='advanced':
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66 #if $adv_opts.param_force:
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67 -force
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68 #end if
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69 #end if
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70 </command>
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71 <inputs>
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72 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input files separated by blank" help="(-in) ">
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73 <sanitizer>
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74 <valid initial="string.printable">
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75 <remove value="'"/>
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76 <remove value="&quot;"/>
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77 </valid>
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78 </sanitizer>
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79 </param>
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80 <param name="param_tr" type="data" format="tabular,traml" optional="False" label="transition file ('TraML' or 'csv')" help="(-tr) "/>
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81 <param name="param_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="(-rt_norm) "/>
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82 <param name="param_min_upper_edge_dist" type="float" value="0.0" label="Minimal distance to the edge to still consider a precursor, in Thomson" help="(-min_upper_edge_dist) "/>
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83 <param name="param_mz_window" type="float" min="0.0" optional="True" value="0.05" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size," help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side"/>
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84 <param name="param_rt_window" type="float" value="-1.0" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size," help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side"/>
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85 <param name="param_is_swath" display="radio" type="boolean" truevalue="-is_swath" falsevalue="" checked="false" optional="True" label="Set this flag if the data is SWATH data" help="(-is_swath) "/>
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86 <param name="param_ppm" display="radio" type="boolean" truevalue="-ppm" falsevalue="" checked="false" optional="True" label="m/z extraction_window is in ppm" help="(-ppm) "/>
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87 <param name="param_extract_MS1" display="radio" type="boolean" truevalue="-extract_MS1" falsevalue="" checked="false" optional="True" label="Extract the MS1 transitions based on the precursor values in the TraML file" help="(-extract_MS1) "/>
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88 <param name="param_extraction_function" display="radio" type="select" optional="False" value="tophat" label="Function used to extract the signal" help="(-extraction_function) ">
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89 <option value="tophat" selected="true">tophat</option>
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90 <option value="bartlett">bartlett</option>
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91 </param>
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92 <param name="param_model_type" display="radio" type="select" optional="False" value="linear" label="Type of model" help="(-type) ">
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93 <option value="linear" selected="true">linear</option>
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94 <option value="b_spline">b_spline</option>
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95 <option value="interpolated">interpolated</option>
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96 <option value="lowess">lowess</option>
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97 </param>
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98 <param name="param_model_symmetric_regression" display="radio" type="boolean" truevalue="-model:symmetric_regression" falsevalue="" checked="false" optional="True" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'"/>
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99 <expand macro="advanced_options">
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100 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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101 </expand>
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102 </inputs>
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103 <outputs>
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104 <data name="param_out" format="mzml"/>
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105 </outputs>
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106 <help>Extract chromatograms (XIC) from a MS2 map file.
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107
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108
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109 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_OpenSwathChromatogramExtractor.html</help>
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110 </tool>