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

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
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4
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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: [Utilities]-->
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4 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="2.0.0">
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5 <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">IDMassAccuracy</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>IDMassAccuracy
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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 -id_in
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20 #for token in $param_id_in:
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21 $token
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22 #end for
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23 #if $param_precursor_out:
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24 -precursor_out $param_precursor_out
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25 #end if
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26
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27 #if $rep_param_precursor_columns:
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28 -precursor_columns
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29 #for token in $rep_param_precursor_columns:
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30 #if &quot; &quot; in str(token):
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31 &quot;$token.param_precursor_columns&quot;
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32 #else
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33 $token.param_precursor_columns
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34 #end if
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35 #end for
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36 #end if
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37 #if $param_precursor_error_ppm:
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38 -precursor_error_ppm
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39 #end if
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40 #if $param_fragment_out:
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41 -fragment_out $param_fragment_out
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42 #end if
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43
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44 #if $rep_param_fragment_columns:
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45 -fragment_columns
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46 #for token in $rep_param_fragment_columns:
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47 #if &quot; &quot; in str(token):
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48 &quot;$token.param_fragment_columns&quot;
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49 #else
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50 $token.param_fragment_columns
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51 #end if
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52 #end for
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53 #end if
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54 #if $param_fragment_error_ppm:
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55 -fragment_error_ppm
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56 #end if
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57 #if $param_fragment_mass_tolerance:
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58 -fragment_mass_tolerance $param_fragment_mass_tolerance
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59 #end if
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60 #if $param_separator:
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61 -separator &quot;$param_separator&quot;
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62 #end if
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63 -threads \${GALAXY_SLOTS:-24}
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64 #if $adv_opts.adv_opts_selector=='advanced':
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65 #if $adv_opts.param_number_of_bins:
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66 -number_of_bins $adv_opts.param_number_of_bins
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67 #end if
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68 #if $adv_opts.param_generate_gnuplot_scripts:
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69 -generate_gnuplot_scripts
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70 #end if
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71 #if $adv_opts.param_force:
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72 -force
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73 #end if
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74 #end if
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75 </command>
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76 <inputs>
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77 <param format="mzml" help="(-in) " label="Input mzML file list, containing the spectra" multiple="true" name="param_in" optional="False" size="30" type="data">
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78 <sanitizer>
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79 <valid initial="string.printable">
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80 <remove value="'"/>
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81 <remove value="&quot;"/>
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82 </valid>
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83 </sanitizer>
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84 </param>
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85 <param format="xml" help="(-id_in) " label="Input idXML file list, containing the identifications" multiple="true" name="param_id_in" optional="False" size="30" type="data">
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86 <sanitizer>
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87 <valid initial="string.printable">
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88 <remove value="'"/>
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89 <remove value="&quot;"/>
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90 </valid>
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91 </sanitizer>
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92 </param>
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93 <repeat max="1" min="0" name="rep_param_precursor_columns" title="param_precursor_columns">
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94 <param help="(-precursor_columns) " label="Columns which will be written to the output file" name="param_precursor_columns" size="30" type="text" value="MassDifference">
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95 <sanitizer>
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96 <valid initial="string.printable">
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97 <remove value="'"/>
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98 <remove value="&quot;"/>
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99 </valid>
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100 </sanitizer>
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101 </param>
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102 </repeat>
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103 <param checked="false" falsevalue="" help="(-precursor_error_ppm) " label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" name="param_precursor_error_ppm" optional="True" truevalue="-precursor_error_ppm" type="boolean"/>
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104 <repeat max="1" min="0" name="rep_param_fragment_columns" title="param_fragment_columns">
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105 <param help="(-fragment_columns) " label="Columns which will be written to the output file" name="param_fragment_columns" size="30" type="text" value="MassDifference">
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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="&quot;"/>
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110 </valid>
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111 </sanitizer>
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112 </param>
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113 </repeat>
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114 <param checked="false" falsevalue="" help="(-fragment_error_ppm) " label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" name="param_fragment_error_ppm" optional="True" truevalue="-fragment_error_ppm" type="boolean"/>
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115 <param help="(-fragment_mass_tolerance) " label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" name="param_fragment_mass_tolerance" type="float" value="0.5"/>
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116 <param help="(-separator) " label="character which should be used to separate the columns in the output files" name="param_separator" size="30" type="text" value=" ">
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117 <sanitizer>
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118 <valid initial="string.printable">
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119 <remove value="'"/>
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120 <remove value="&quot;"/>
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121 </valid>
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122 </sanitizer>
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123 </param>
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124 <expand macro="advanced_options">
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125 <param help="(-number_of_bins) " label="Number of bins that should be used to calculate the histograms for the fitting" min="10" name="param_number_of_bins" optional="True" type="integer" value="100"/>
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126 <param checked="false" falsevalue="" help="(-generate_gnuplot_scripts) The options 'precursor_out' and 'fragment_out' must be set to take this effect" 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" name="param_generate_gnuplot_scripts" optional="True" truevalue="-generate_gnuplot_scripts" type="boolean"/>
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127 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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128 </expand>
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129 </inputs>
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130 <outputs>
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131 <data format="tabular" name="param_precursor_out"/>
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132 <data format="tabular" name="param_fragment_out"/>
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133 </outputs>
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134 <help>Calculates a distribution of the mass error from given mass spectra and IDs.
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135
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136
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137 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_IDMassAccuracy.html</help>
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138 </tool>