Mercurial > repos > galaxyp > openms_masscalculator

annotate MassCalculator.xml @ 2:9b8cd97fa5d0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 1e51bed3a1c10c67ef0404216608e9333db04c64
author galaxyp
date Wed, 18 Oct 2017 15:47:06 -0400
parents 7d95120eee87
children 7db481946a90
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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="MassCalculator" name="MassCalculator" version="2.2.0">
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5 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MassCalculator</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>MassCalculator
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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19 #if $rep_param_in_seq:
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20 -in_seq
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21 #for token in $rep_param_in_seq:
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22 #if " " in str(token):
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23 "$token.param_in_seq"
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24 #else
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25 $token.param_in_seq
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26 #end if
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27 #end for
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28 #end if
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29 #if $param_out:
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30 -out $param_out
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31 #end if
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32
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33 #if $rep_param_charge:
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34 -charge
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35 #for token in $rep_param_charge:
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36 #if " " in str(token):
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37 "$token.param_charge"
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38 #else
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39 $token.param_charge
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40 #end if
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41 #end for
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42 #end if
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43 #if $param_format:
1
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44 -format
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45 #if " " in str($param_format):
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46 "$param_format"
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47 #else
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48 $param_format
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49 #end if
0
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50 #end if
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51 #if $param_average_mass:
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52 -average_mass
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53 #end if
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54 #if $param_fragment_type:
1
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55 -fragment_type
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56 #if " " in str($param_fragment_type):
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57 "$param_fragment_type"
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58 #else
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59 $param_fragment_type
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60 #end if
0
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61 #end if
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62 #if $param_separator:
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63 -separator "$param_separator"
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64 #end if
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65 #if $adv_opts.adv_opts_selector=='advanced':
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66 #if $adv_opts.param_force:
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67 -force
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68 #end if
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69 #end if
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70 </command>
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71 <inputs>
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72 <param name="param_in" type="data" format="txt" optional="True" label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" help="(-in) "/>
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73 <repeat name="rep_param_in_seq" min="0" max="1" title="param_in_seq">
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74 <param name="param_in_seq" type="text" size="30" label="List of peptide sequences (mutually exclusive to 'in')" help="(-in_seq) ">
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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="&quot;"/>
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79 </valid>
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80 </sanitizer>
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81 </param>
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82 </repeat>
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83 <repeat name="rep_param_charge" min="0" max="1" title="param_charge">
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84 <param name="param_charge" type="text" size="30" value="0" label="List of charge states; required if 'in_seq' is given" help="(-charge) ">
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85 <sanitizer>
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86 <valid initial="string.printable">
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87 <remove value="'"/>
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88 <remove value="&quot;"/>
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89 </valid>
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90 </sanitizer>
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91 </param>
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92 </repeat>
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93 <param name="param_format" display="radio" type="select" optional="False" value="list" label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" help="(-format) ">
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94 <option value="list" selected="true">list</option>
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95 <option value="table">table</option>
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96 <option value="mass_only">mass_only</option>
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97 <option value="mz_only">mz_only</option>
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98 </param>
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99 <param name="param_average_mass" display="radio" type="boolean" truevalue="-average_mass" falsevalue="" checked="false" optional="True" label="Compute average (instead of monoisotopic) peptide masses" help="(-average_mass) "/>
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100 <param name="param_fragment_type" type="select" optional="False" value="full" label="For what type of sequence/fragment the mass should be computed" help="(-fragment_type) ">
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101 <option value="full" selected="true">full</option>
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102 <option value="internal">internal</option>
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103 <option value="N-terminal">N-terminal</option>
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104 <option value="C-terminal">C-terminal</option>
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105 <option value="a-ion">a-ion</option>
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106 <option value="b-ion">b-ion</option>
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107 <option value="c-ion">c-ion</option>
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108 <option value="x-ion">x-ion</option>
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109 <option value="y-ion">y-ion</option>
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110 <option value="z-ion">z-ion</option>
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111 </param>
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112 <param name="param_separator" type="text" size="30" label="Field separator for 'table' output format; by default, the 'tab' character is used" help="(-separator) ">
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113 <sanitizer>
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114 <valid initial="string.printable">
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115 <remove value="'"/>
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116 <remove value="&quot;"/>
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117 </valid>
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118 </sanitizer>
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119 </param>
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120 <expand macro="advanced_options">
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121 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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122 </expand>
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123 </inputs>
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124 <outputs>
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125 <data name="param_out" format="txt"/>
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126 </outputs>
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127 <help>Calculates masses and mass-to-charge ratios of peptide sequences
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128
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129
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130 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html</help>
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131 </tool>