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1 <tool id="msconvert_subset" name="Subset Peak List" version="0.1.0">
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2 <description>against list of scan numbers or indices.</description>
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3 <command interpreter="python">
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4 msconvert_wrapper.py
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5 --input=${input}
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6 --output=${output}
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7 --fromextension=${input.ext}
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8 --toextension=${output_type}
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9 #if $settings.settingsType == "full"
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10 --binaryencoding=${settings.binary_encoding}
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11 --mzencoding=${settings.mz_encoding}
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12 --intensityencoding=${settings.intensity_encoding}
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13 --zlib=${settings.zlib}
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14 #end if
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15 --filter_table="$filter.filterList"
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16 #if $filter.filterType == "scan_number"
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17 --filter_table_type="number"
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18 #else
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19 --filter_table_type="index"
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20 #end if
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21 </command>
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22
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23 <inputs>
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24 <conditional name="type">
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25 <param name="input_type" type="select" label="Input Type">
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26 <option value="mzml">mzML</option>
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27 <option value="mzxml">mzXML</option>
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28 <option value="mgf">mgf</option>
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29 <option value="ms2">ms2</option>
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30 </param>
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31 <when value="mzml">
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32 <param format="mzml" name="input" type="data" label="Input mzML"/>
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33 </when>
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34 <when value="mzxml">
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35 <param format="mzxml" name="input" type="data" label="Input mzXML"/>
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36 </when>
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37 <when value="mgf">
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38 <param format="mgf" name="input" type="data" label="Input mgf"/>
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39 </when>
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40 <when value="ms2">
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41 <param format="ms2" name="input" type="data" label="Input ms2"/>
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42 </when>
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43 </conditional>
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44 <param name="output_type" type="select" label="Output Type">
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45 <option value="mzML">mzML (indexed)</option>
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46 <option value="unindexed_mzML">mzML (unindexed)</option>
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47 <option value="mzXML">mzXML (indexed)</option>
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48 <option value="unindexed_mzXML">mzXML (unindexed)</option>
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49 <option value="mgf">mgf</option>
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50 <option value="ms2">ms2</option>
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51 </param>
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52 <conditional name="filter">
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53 <param name="filterType" type="select" label="Filter by" help="">
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54 <option value="scan_number" selected="true">Scan Number</option>
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55 <option value="scan_index">Scan Index</option>
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56 </param>
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57 <when value="scan_number">
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58 <param format="text" name="filterList" type="data" label="Scan Numbers"/>
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59 </when>
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60 <when value="scan_index">
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61 <param format="text" name="filterList" type="data" label="Scan Indices"/>
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62 </when>
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63 </conditional>
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64 <conditional name="settings">
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65 <param name="settingsType" type="select" label="Advanced msconvert Settings" help="">
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66 <option value="default">Use Defaults</option>
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67 <option value="full">Full Parameter List</option>
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68 </param>
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69 <when value="default" />
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70 <when value="full">
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71 <param type="select" name="binary_encoding" label="Binary Encoding Precision">
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72 <option value="64" selected="true">64</option>
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73 <option value="32">32</option>
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74 </param>
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75 <param type="select" name="mz_encoding" label="m/z Encoding Precision">
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76 <option value="64" selected="true">64</option>
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77 <option value="32">32</option>
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78 </param>
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79 <param type="select" name="intensity_encoding" label="Intensity Encoding Precision" value="32">
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80 <option value="64">64</option>
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81 <option value="32" selected="true">32</option>
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82 </param>
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83 <param type="boolean" name="zlib" label="Use zlib">
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84 </param>
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85 </when>
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86 </conditional>
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87 </inputs>
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88 <outputs>
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89 <data format="mzml" name="output">
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90 <change_format>
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91 <when input="output_type" value="mzXML" format="mzxml" />
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92 <when input="output_type" value="unindexed_mzXML" format="mzxml" />
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93 <when input="output_type" value="ms2" format="ms2" />
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94 <when input="output_type" value="mgf" format="mgf" />
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95 </change_format>
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96 </data>
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97 </outputs>
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98
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99 <requirements>
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100 <requirement type="package">proteowizard</requirement>
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101 </requirements>
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102
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103 <help>
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104 </help>
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105 </tool>
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