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annotate MassCalculator.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
parents 3d84209d3178
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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="MassCalculator" name="MassCalculator" version="2.0.0">
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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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18
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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 $rep_param_in_seq:
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22 #if &quot; &quot; in str(token):
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23 &quot;$token.param_in_seq&quot;
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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
0
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32
4
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33 #if $rep_param_charge:
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34 -charge
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35 #for token in $rep_param_charge:
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36 #if &quot; &quot; in str(token):
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37 &quot;$token.param_charge&quot;
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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 $param_format:
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44 -format
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45 #if &quot; &quot; in str($param_format):
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46 &quot;$param_format&quot;
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47 #else
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48 $param_format
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49 #end if
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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 $param_fragment_type:
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55 -fragment_type
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56 #if &quot; &quot; in str($param_fragment_type):
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57 &quot;$param_fragment_type&quot;
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58 #else
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59 $param_fragment_type
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60 #end if
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61 #end if
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62 #if $param_separator:
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63 -separator &quot;$param_separator&quot;
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64 #end if
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65 -threads \${GALAXY_SLOTS:-24}
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66 #if $adv_opts.adv_opts_selector=='advanced':
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67 #if $adv_opts.param_force:
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68 -force
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69 #end if
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70 #end if
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71 </command>
4
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72 <inputs>
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73 <param format="txt" help="(-in) " label="Input file with peptide sequences and optionally charge numbers (mutually exclusive to 'in_seq')" name="param_in" optional="True" type="data"/>
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74 <repeat min="0" name="rep_param_in_seq" title="param_in_seq">
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75 <param help="(-in_seq) " label="List of peptide sequences (mutually exclusive to 'in')" name="param_in_seq" size="30" type="text">
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76 <sanitizer>
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77 <valid initial="string.printable">
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78 <remove value="'"/>
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79 <remove value="&quot;"/>
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80 </valid>
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81 </sanitizer>
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82 </param>
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83 </repeat>
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84 <repeat max="1" min="0" name="rep_param_charge" title="param_charge">
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85 <param help="(-charge) " label="List of charge states; required if 'in_seq' is given" name="param_charge" size="30" type="text" value="0">
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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>
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94 <param help="(-format) " label="Output format ('list': human-readable list, 'table': CSV-like table, 'mass_only': mass values only, 'mz_only': m/z values only)" name="param_format" optional="True" type="select" value="list">
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95 <option value="list">list</option>
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96 <option value="table">table</option>
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97 <option value="mass_only">mass_only</option>
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98 <option value="mz_only">mz_only</option>
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99 </param>
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100 <param checked="false" falsevalue="" help="(-average_mass) " label="Compute average (instead of monoisotopic) peptide masses" name="param_average_mass" optional="True" truevalue="-average_mass" type="boolean"/>
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101 <param help="(-fragment_type) " label="For what type of sequence/fragment the mass should be computed" name="param_fragment_type" optional="True" type="select" value="full">
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102 <option value="full">full</option>
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103 <option value="internal">internal</option>
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104 <option value="N-terminal">N-terminal</option>
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105 <option value="C-terminal">C-terminal</option>
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106 <option value="a-ion">a-ion</option>
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107 <option value="b-ion">b-ion</option>
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108 <option value="c-ion">c-ion</option>
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109 <option value="x-ion">x-ion</option>
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110 <option value="y-ion">y-ion</option>
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111 <option value="z-ion">z-ion</option>
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112 </param>
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113 <param help="(-separator) " label="Field separator for 'table' output format; by default, the 'tab' character is used" name="param_separator" size="30" type="text">
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114 <sanitizer>
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115 <valid initial="string.printable">
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116 <remove value="'"/>
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117 <remove value="&quot;"/>
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118 </valid>
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119 </sanitizer>
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120 </param>
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121 <expand macro="advanced_options">
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122 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
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123 </expand>
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124 </inputs>
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125 <outputs>
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126 <data format="txt" name="param_out"/>
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127 </outputs>
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128 <help>Calculates masses and mass-to-charge ratios of peptide sequences
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129
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130
4
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131 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_MassCalculator.html</help>
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132 </tool>