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

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author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
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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: [Quantitation]-->
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4 <tool id="EICExtractor" name="EICExtractor" version="2.0.0">
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5 <description>Extracts intensities from dedicates positions in a LC/MS map</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">EICExtractor</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>EICExtractor
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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 -in_header
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20 #for token in $param_in_header:
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21 $token
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22 #end for
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23 #if $param_pos:
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24 -pos $param_pos
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25 #end if
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26 #if $param_rt_tol:
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27 -rt_tol $param_rt_tol
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28 #end if
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29 #if $param_mz_tol:
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30 -mz_tol $param_mz_tol
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31 #end if
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32 #if $param_rt_collect:
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33 -rt_collect $param_rt_collect
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34 #end if
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35 #if $param_out:
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36 -out $param_out
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37 #end if
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38 -threads \${GALAXY_SLOTS:-24}
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39 #if $param_auto_rt_enabled:
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40 -auto_rt:enabled
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41 #end if
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42 #if $param_auto_rt_out_debug_TIC:
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43 -auto_rt:out_debug_TIC $param_auto_rt_out_debug_TIC
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44 #end if
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45 #if $adv_opts.adv_opts_selector=='advanced':
4
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46 #if $adv_opts.param_out_separator:
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47 -out_separator &quot;$adv_opts.param_out_separator&quot;
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48 #end if
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49 #if $adv_opts.param_force:
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50 -force
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51 #end if
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52 #if $adv_opts.param_auto_rt_FHWM:
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53 -auto_rt:FHWM $adv_opts.param_auto_rt_FHWM
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54 #end if
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55 #if $adv_opts.param_auto_rt_SNThreshold:
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56 -auto_rt:SNThreshold $adv_opts.param_auto_rt_SNThreshold
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57 #end if
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58 #end if
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59 </command>
4
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60 <inputs>
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61 <param format="mzml" help="(-in) " label="Input raw data file" multiple="true" name="param_in" optional="False" size="30" type="data">
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62 <sanitizer>
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63 <valid initial="string.printable">
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64 <remove value="'"/>
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65 <remove value="&quot;"/>
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66 </valid>
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67 </sanitizer>
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68 </param>
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69 <param format="txt" help="(-in_header) Provide one for each raw input file" label="[for Waters data only] Read additional information from _HEADER.TXT" multiple="true" name="param_in_header" optional="True" size="30" type="data">
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70 <sanitizer>
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71 <valid initial="string.printable">
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72 <remove value="'"/>
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73 <remove value="&quot;"/>
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74 </valid>
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75 </sanitizer>
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76 </param>
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77 <param format="tabular" help="(-pos) " label="Input config file stating where to find signal" name="param_pos" optional="False" type="data"/>
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78 <param help="(-rt_tol) " label="RT tolerance in [s] for finding max peak (whole RT range around RT middle)" name="param_rt_tol" type="float" value="3.0"/>
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79 <param help="(-mz_tol) " label="m/z tolerance in [ppm] for finding a peak" name="param_mz_tol" type="float" value="10.0"/>
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80 <param help="(-rt_collect) " label="# of scans up &amp; down in RT from highest point for ppm estimation in result" name="param_rt_collect" type="integer" value="1"/>
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81 <param checked="false" falsevalue="" help="(-enabled) " label="Automatically detect injection peaks from TIC and quantify all m/z x RT combinations" name="param_auto_rt_enabled" optional="True" truevalue="-auto_rt:enabled" type="boolean"/>
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82 <expand macro="advanced_options">
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83 <param help="(-out_separator) " label="Separator character for output CSV file" name="param_out_separator" size="30" type="text" value=",">
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84 <sanitizer>
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85 <valid initial="string.printable">
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86 <remove value="'"/>
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87 <remove value="&quot;"/>
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88 </valid>
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89 </sanitizer>
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90 </param>
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91 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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92 <param help="(-FHWM) Gaussian smoothing filter with this width is applied to TIC" label="Expected full width at half-maximum of each raw RT peak in [s]" name="param_auto_rt_FHWM" type="float" value="5.0"/>
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93 <param help="(-SNThreshold) Higher thesholds will result in less peaks" label="S/N threshold for a smoothed raw peak to pass peak picking" name="param_auto_rt_SNThreshold" type="float" value="5.0"/>
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94 </expand>
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95 </inputs>
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96 <outputs>
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97 <data format="tabular" name="param_out"/>
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98 <data format="mzml" name="param_auto_rt_out_debug_TIC"/>
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99 </outputs>
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100 <help>Extracts intensities from dedicates positions in a LC/MS map
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101
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102
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103 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_EICExtractor.html</help>
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104 </tool>