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annotate OpenSwathChromatogramExtractor.xml @ 4:6ead64a594bd draft default tip

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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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="2.0.0">
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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 $param_extraction_function:
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47 -extraction_function
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48 #if &quot; &quot; in str($param_extraction_function):
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49 &quot;$param_extraction_function&quot;
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50 #else
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51 $param_extraction_function
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52 #end if
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53 #end if
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54 -threads \${GALAXY_SLOTS:-24}
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55 #if $param_model_type:
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56 -model:type
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57 #if &quot; &quot; in str($param_model_type):
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58 &quot;$param_model_type&quot;
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59 #else
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60 $param_model_type
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61 #end if
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62 #end if
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63 #if $param_model_symmetric_regression:
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64 -model:symmetric_regression
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65 #end if
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66 #if $adv_opts.adv_opts_selector=='advanced':
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67 #if $adv_opts.param_force:
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68 -force
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69 #end if
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70 #end if
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71 </command>
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72 <inputs>
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73 <param format="mzml" help="(-in) " label="Input files separated by blank" multiple="true" name="param_in" optional="False" size="30" type="data">
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74 <sanitizer>
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75 <valid initial="string.printable">
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76 <remove value="'"/>
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77 <remove value="&quot;"/>
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78 </valid>
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79 </sanitizer>
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80 </param>
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81 <param format="tabular,traml" help="(-tr) " label="transition file ('TraML' or 'csv')" name="param_tr" optional="False" type="data"/>
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82 <param format="trafoxml" help="(-rt_norm) " label="RT normalization file (how to map the RTs of this run to the ones stored in the library)" name="param_rt_norm" optional="True" type="data"/>
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83 <param help="(-min_upper_edge_dist) " label="Minimal distance to the edge to still consider a precursor, in Thomson" name="param_min_upper_edge_dist" type="float" value="0.0"/>
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84 <param help="(-mz_window) e.g. 100 ppm would extract 50 ppm on either side" label="Extraction window in m/z dimension (in Thomson, to use ppm see -ppm flag). This is the full window size," min="0.0" name="param_mz_window" optional="True" type="float" value="0.05"/>
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85 <param help="(-rt_window) e.g. a value of 1000 seconds would extract 500 seconds on either side" label="Extraction window in RT dimension (-1 means extract over the whole range). This is the full window size," name="param_rt_window" type="float" value="-1.0"/>
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86 <param checked="false" falsevalue="" help="(-is_swath) " label="Set this flag if the data is SWATH data" name="param_is_swath" optional="True" truevalue="-is_swath" type="boolean"/>
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87 <param checked="false" falsevalue="" help="(-ppm) " label="m/z extraction_window is in ppm" name="param_ppm" optional="True" truevalue="-ppm" type="boolean"/>
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88 <param checked="false" falsevalue="" help="(-extract_MS1) " label="Extract the MS1 transitions based on the precursor values in the TraML file" name="param_extract_MS1" optional="True" truevalue="-extract_MS1" type="boolean"/>
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89 <param help="(-extraction_function) " label="Function used to extract the signal" name="param_extraction_function" optional="True" type="select" value="tophat">
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90 <option value="tophat">tophat</option>
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91 <option value="bartlett">bartlett</option>
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92 </param>
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93 <param help="(-type) " label="Type of model" name="param_model_type" optional="True" type="select" value="linear">
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94 <option value="linear">linear</option>
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95 <option value="b_spline">b_spline</option>
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96 <option value="interpolated">interpolated</option>
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97 </param>
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98 <param checked="false" falsevalue="" help="(-symmetric_regression) 'y + x', instead of on 'y' vs. 'x'" label="Only for 'linear' model: Perform linear regression on 'y - x' vs" name="param_model_symmetric_regression" optional="True" truevalue="-model:symmetric_regression" type="boolean"/>
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99 <expand macro="advanced_options">
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100 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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101 </expand>
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102 </inputs>
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103 <outputs>
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104 <data format="mzml" name="param_out"/>
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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
4
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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>