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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="2.0.0">
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3 <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">IDMassAccuracy</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>IDMassAccuracy
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11
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12 -in
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13 #for token in $param_in:
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14 $token
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15 #end for
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16 -id_in
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17 #for token in $param_id_in:
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18 $token
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19 #end for
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20 #if $param_precursor_out:
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21 -precursor_out $param_precursor_out
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22 #end if
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23
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24 #if $rep_param_precursor_columns:
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25 -precursor_columns
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26 #for token in $rep_param_precursor_columns:
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27 #if " " in str(token):
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28 "$token.param_precursor_columns"
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29 #else
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30 $token.param_precursor_columns
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31 #end if
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32 #end for
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33 #end if
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34 #if $param_precursor_error_ppm:
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35 -precursor_error_ppm
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36 #end if
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37 #if $param_fragment_out:
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38 -fragment_out $param_fragment_out
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39 #end if
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40
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41 #if $rep_param_fragment_columns:
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42 -fragment_columns
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43 #for token in $rep_param_fragment_columns:
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44 #if " " in str(token):
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45 "$token.param_fragment_columns"
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46 #else
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47 $token.param_fragment_columns
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48 #end if
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49 #end for
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50 #end if
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51 #if $param_fragment_error_ppm:
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52 -fragment_error_ppm
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53 #end if
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54 #if $param_fragment_mass_tolerance:
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55 -fragment_mass_tolerance $param_fragment_mass_tolerance
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56 #end if
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57 #if $param_separator:
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58 -separator "$param_separator"
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59 #end if
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60 -threads \${GALAXY_SLOTS:-24}
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61 #if $adv_opts.adv_opts_selector=='advanced':
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62 #if $adv_opts.param_number_of_bins:
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63 -number_of_bins $adv_opts.param_number_of_bins
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64 #end if
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65 #if $adv_opts.param_generate_gnuplot_scripts:
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66 -generate_gnuplot_scripts
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67 #end if
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68 #if $adv_opts.param_force:
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69 -force
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70 #end if
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71 #end if
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72 </command>
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73 <inputs>
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74 <param name="param_in" type="data" format="mzml" multiple="true" optional="False" size="30" label="Input mzML file list, containing the spectra" help="(-in) ">
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75 <sanitizer>
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76 <valid initial="string.printable">
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77 <remove value="'"/>
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78 <remove value="""/>
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79 </valid>
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80 </sanitizer>
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81 </param>
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82 <param name="param_id_in" type="data" format="idxml" multiple="true" optional="False" size="30" label="Input idXML file list, containing the identifications" help="(-id_in) ">
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83 <sanitizer>
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84 <valid initial="string.printable">
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85 <remove value="'"/>
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86 <remove value="""/>
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87 </valid>
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88 </sanitizer>
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89 </param>
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90 <repeat name="rep_param_precursor_columns" min="0" max="1" title="param_precursor_columns">
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91 <param name="param_precursor_columns" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-precursor_columns) ">
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92 <option value="MassDifference">MassDifference</option>
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93 <option value="none">none</option>
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94 </param>
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95 </repeat>
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96 <param name="param_precursor_error_ppm" type="boolean" truevalue="-precursor_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help="(-precursor_error_ppm) "/>
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97 <repeat name="rep_param_fragment_columns" min="0" max="1" title="param_fragment_columns">
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98 <param name="param_fragment_columns" type="select" optional="True" value="MassDifference" label="Columns which will be written to the output file" help="(-fragment_columns) ">
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99 <option value="MassDifference">MassDifference</option>
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100 <option value="none">none</option>
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101 </param>
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102 </repeat>
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103 <param name="param_fragment_error_ppm" type="boolean" truevalue="-fragment_error_ppm" falsevalue="" checked="false" optional="True" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help="(-fragment_error_ppm) "/>
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104 <param name="param_fragment_mass_tolerance" type="float" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help="(-fragment_mass_tolerance) "/>
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105 <param name="param_separator" type="text" size="30" value=" " label="character which should be used to separate the columns in the output files" help="(-separator) ">
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106 <sanitizer>
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107 <valid initial="string.printable">
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108 <remove value="'"/>
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109 <remove value="""/>
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110 </valid>
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111 </sanitizer>
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112 </param>
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113 <expand macro="advanced_options">
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114 <param name="param_number_of_bins" type="integer" min="10" optional="True" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help="(-number_of_bins) "/>
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115 <param name="param_generate_gnuplot_scripts" type="boolean" truevalue="-generate_gnuplot_scripts" falsevalue="" checked="false" optional="True" label="If this option is set to true, the distributions and the fits are used to generate a gnuplot script, that can be used to generate plots" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect"/>
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116 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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117 </expand>
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118 </inputs>
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119 <outputs>
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120 <data name="param_precursor_out" format="tabular"/>
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121 <data name="param_fragment_out" format="tabular"/>
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122 </outputs>
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123 <help>**What it does**
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124
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125 Calculates a distribution of the mass error from given mass spectra and IDs.
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126
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127
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128 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDMassAccuracy.html</help>
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129 <expand macro="references"/>
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130 </tool>
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