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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="MassCalculator" name="MassCalculator" version="2.0.0">
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3 <description>Calculates masses and mass-to-charge ratios of peptide sequences</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">MassCalculator</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>MassCalculator
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11
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12 #if $param_in:
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13 -in $param_in
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14 #end if
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15
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16 #if $rep_param_in_seq:
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17 -in_seq
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18 #for token in $rep_param_in_seq:
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19 #if " " in str(token):
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20 "$token.param_in_seq"
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21 #else
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22 $token.param_in_seq
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23 #end if
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24 #end for
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25 #end if
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26 #if $param_out:
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27 -out $param_out
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28 #end if
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29
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30 #if $rep_param_charge:
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31 -charge
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32 #for token in $rep_param_charge:
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33 #if " " in str(token):
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34 "$token.param_charge"
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35 #else
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36 $token.param_charge
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37 #end if
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38 #end for
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39 #end if
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40 #if $param_format:
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41 -format
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42 #if " " in str($param_format):
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43 "$param_format"
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44 #else
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45 $param_format
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46 #end if
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47 #end if
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48 #if $param_average_mass:
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49 -average_mass
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50 #end if
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51 #if $param_fragment_type:
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52 -fragment_type
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53 #if " " in str($param_fragment_type):
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54 "$param_fragment_type"
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55 #else
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56 $param_fragment_type
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57 #end if
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58 #end if
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59 #if $param_separator:
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60 -separator "$param_separator"
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61 #end if
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62 -threads \${GALAXY_SLOTS:-24}
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63 #if $adv_opts.adv_opts_selector=='advanced':
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64 #if $adv_opts.param_force:
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65 -force
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66 #end if
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67 #end if
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68 </command>
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69 <inputs>
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70 <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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71 <repeat name="rep_param_in_seq" min="0" title="param_in_seq">
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72 <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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73 <sanitizer>
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74 <valid initial="string.printable">
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75 <remove value="'"/>
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76 <remove value="""/>
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77 </valid>
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78 </sanitizer>
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79 </param>
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80 </repeat>
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81 <repeat name="rep_param_charge" min="0" max="1" title="param_charge">
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82 <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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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>
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91 <param name="param_format" type="select" optional="True" 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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92 <option value="list">list</option>
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93 <option value="table">table</option>
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94 <option value="mass_only">mass_only</option>
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95 <option value="mz_only">mz_only</option>
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96 </param>
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97 <param name="param_average_mass" 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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98 <param name="param_fragment_type" type="select" optional="True" value="full" label="For what type of sequence/fragment the mass should be computed" help="(-fragment_type) ">
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99 <option value="full">full</option>
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100 <option value="internal">internal</option>
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101 <option value="N-terminal">N-terminal</option>
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102 <option value="C-terminal">C-terminal</option>
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103 <option value="a-ion">a-ion</option>
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104 <option value="b-ion">b-ion</option>
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105 <option value="c-ion">c-ion</option>
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106 <option value="x-ion">x-ion</option>
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107 <option value="y-ion">y-ion</option>
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108 <option value="z-ion">z-ion</option>
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109 </param>
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110 <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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111 <sanitizer>
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112 <valid initial="string.printable">
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113 <remove value="'"/>
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114 <remove value="""/>
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115 </valid>
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116 </sanitizer>
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117 </param>
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118 <expand macro="advanced_options">
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119 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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120 </expand>
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121 </inputs>
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122 <outputs>
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123 <data name="param_out" format="txt"/>
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124 </outputs>
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125 <help>**What it does**
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126
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127 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 <expand macro="references"/>
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132 </tool>
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