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1 <tool id="hr2" name="HR2 formula" version="1.1.1.7">
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2 <description>
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3 find a chemical formula from a accurate mass
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="2.161">perl-data-dumper</requirement>
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7 <requirement type="package" version="1.97">perl-text-csv</requirement>
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8 <requirement type="package" version="2.97">perl-html-template</requirement>
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9 <requirement type="package" version="1.04">hr2</requirement>
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10 </requirements>
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11 <stdio>
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12 <exit_code range="1" level="fatal" />
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13 </stdio>
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14
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15
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16 <command><![CDATA[
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17 perl $__tool_directory__/hr2_manager.pl
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18 #if str($input_type.choice) == "YES":
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19 -input "${input_type.input}"
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20 #if str($input_type.header.header_choice) == "yes":
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21 -nblineheader "${$input_type.header.nbHeader}"
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22 #end if
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23 -colId "${input_type.colId}" -colmass "${input_type.colmass}"
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24 #else:
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25 -masse "${input_type.masse}"
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26 #end if
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27
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28 -tolerance "$tol"
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29 -mode "${mode_condition.mode}"
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30 #if str($mode_condition.mode) == "neutral":
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31 -charge "0"
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32 #else:
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33 -charge "${mode_condition.qtCharge}"
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34 #end if
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35
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36 -regleOr "$regleOr" -atomes "$atomes_basic" -atomessup "$atomes_sup"
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37 -output1 "$variableMetadata" -outputView "$hr2ResView"
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38 -verbose "$verbose"
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39 ]]></command>
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40
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41 <inputs>
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42 <conditional name="input_type">
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43 <param name="choice" type="select" display="radio" label="Would you use a file " help="if 'NO' is selected then one or more mass(es) must be entered manually">
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44 <option value="YES">YES</option>
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45 <option value="NO">NO</option>
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46 </param>
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47 <when value="YES">
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48 <param name="input" label="File of masses" format="tabular" type="data" />
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49 <conditional name="header">
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50 <param name="header_choice" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Do you have a header?" help="if 'YES' is selected then enter your number of header lines" />
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51 <when value="yes">
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52 <param name="nbHeader" label="Number of header lines" type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/>
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53 </when>
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54 <when value="no"/>
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55 </conditional>
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56 <param name="colId" label="Column of Id" type="data_column" data_ref="input" accept_default="true" />
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57 <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="input" accept_default="true" />
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58 </when>
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59 <when value="NO">
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60 <param name="masse" size="20" type="text" label="Mass (MZ) to submit" help="For a masses list, writes : m1 m2 m3. Your values must be separated by spaces. You should use dot (.) like decimal separator"/>
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61 </when>
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62 </conditional>
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63
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64 <param name="tol" label="Delta of mass (MZ) (in mmu)" type="float" value="1.0" min="0" max="9.0" help="Tolerance should be between 0 and 9.0 mmu. Default value is 1.0 mmu"/>
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65 <conditional name="mode_condition">
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66 <param name="mode" label="Molecular Species Searched" type="select" display="radio" help="Or ionization type of the molecule list. Use neutral only if only if the masses correspond to molecules and not to ions : query doesn't be a [M+H] or [M-H] ion">
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67 <option value="positive">positive</option>
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68 <option value="negative">negative</option>
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69 <option value="neutral" selected="true">neutral</option>
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70 </param>
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71 <when value="neutral"/>
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72 <when value="positive">
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73 <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged">
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74 <option value="1">1</option>
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75 <option value="2">2</option>
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76 <option value="3">3</option>
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77 </param>
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78 </when>
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79 <when value="negative">
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80 <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged">
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81 <option value="1">1</option>
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82 <option value="2">2</option>
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83 <option value="3">3</option>
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84 </param>
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85 </when>
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86 </conditional>
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87 <param name="atomes_basic" label="Please unselect basic atom(s) from following list you want to exclude" type="select" display="checkboxes" multiple="True" help="Unselect one or more basic atoms to exclude them from the generated formula proposition">
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88 <option value="C" selected="true">C</option>
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89 <option value="N" selected="true">N</option>
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90 <option value="O" selected="true">O</option>
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91 <option value="H" selected="true">H</option>
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92 <option value="P" selected="true">P</option>
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93 </param>
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94 <param name="regleOr" label="Use all 7 golden rules OR only the first 3 golden rules?" type="select" display="radio" help="Use 'only first 3 rules' if you want more empirical formulas">
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95 <option value="YES">only first 3 rules</option>
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96 <option value="NO" selected="true">all 7 rules</option>
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97 </param>
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98 <param name="atomes_sup" label="Add some atom(s) from following list if needed" type="select" display="checkboxes" multiple="True" help="C, H, N, O and P are available in basic atom section">
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99 <option value="S">S</option>
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100 <option value="F">F</option>
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101 <option value="L">Cl</option>
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102 <option value="K">K</option>
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103 <option value="B">Br</option>
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104 <option value="A">Na</option>
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105 <option value="1">13C</option>
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106 </param>
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107 <param name="verbose" type="select" label="Verbose level" display="radio" help="">
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108 <option value="1" selected="true">Low</option>
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109 <option value="3" >High</option>
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110 </param>
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111 </inputs>
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112 <outputs>
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113 <data name="variableMetadata" format="tabular" label="${tool.name}_TSV"/>
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114 <data name="hr2ResView" format="html" label="${tool.name}_VIEW"/>
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115 </outputs>
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116
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117 <tests>
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118 <test>
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119 <param name="choice" value="NO"/>
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120 <param name="masse" value="175.125"/>
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121 <param name="tolerance" value="1.0"/>
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122 <param name="mode" value="negative"/>
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123 <param name="qtCharge" value="1"/>
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124 <param name="atomes_basic" value="C,O,N,H"/>
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125 <param name="regleOr" value="NO"/>
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126 <param name="verbose" value="3"/>
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127 <output name="variableMetadata" file="out_test01.tabular"/>
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128 <output name="hr2ResView" file="out_test01.html"/>
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129 </test>
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130 <test>
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131 <param name="choice" value="NO"/>
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132 <param name="masse" value="88.052"/>
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133 <param name="tolerance" value="1.0"/>
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134 <param name="mode" value="neutral"/>
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135 <param name="qtCharge" value="1"/>
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136 <param name="atomes_basic" value="C,O,H"/>
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137 <param name="regleOr" value="NO"/>
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138 <param name="verbose" value="3"/>
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139 <output name="variableMetadata" file="out_test02.tabular"/>
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140 <output name="hr2ResView" file="out_test02.html"/>
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141 </test>
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142 </tests>
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143
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144 <help><![CDATA[
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145
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146 .. class:: infomark
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147
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148 **Authors**
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149 | HR2 original program and its documentation are Copyright (c) 1992-2005 by Joerg Hau under GNU General Public License ("GPL")
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150
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151 .. class:: infomark
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152
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153 **Wrapping**
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154 | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for xml interface and Perl wrapper)
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155 | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface, conda dependancies and Perl wrapper)
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156
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157 ---------------------------------------------------
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158
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159 .. class:: infomark
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160
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161 **Please cite** If you use this tool, please cite
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162 | Tobias Kind and Oliver Fiehn. (2007). "Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry." BMC Bioinformatics p8:105 http://www.ncbi.nlm.nih.gov/pubmed/17389044
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163 | HR2 original program and its documentation are under GNU General Public License ("GPL") : GPL is a"contaminating" license. http://fiehnlab.ucdavis.edu/projects/Seven_Golden_Rules/Software
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164
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165
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166 ---------------------------------------------------
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167
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168 ==============
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169 HR2 formula
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170 ==============
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171
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172 -----------
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173 Description
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174 -----------
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175
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176 | Find a formula for the masses
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177 | only molecules with carbon (C) will be search
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178
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179
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180 -----------------
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181 Workflow position
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182 -----------------
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183
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184
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185 .. image:: ./static/images/metabolomics/hr2.png
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186 :width: 800
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187
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188
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189
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190
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191 -----------
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192 Input files
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193 -----------
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194
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195 +-------------------------+-----------+
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196 | Parameter : num + label | Format |
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197 +=========================+===========+
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198 | 1 : variableMetadata | tabular |
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199 +-------------------------+-----------+
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200
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201 File variableMetadata must have at least the 2 following columns :
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202 * Id : column to identify masses in the csv/tsv input file
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203 * Masses : column with all the masses in the csv/tsv input file
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204
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205
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206 ----------
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207 Parameters
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208 ----------
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209
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210 Would you use a file
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211 | Choose whether the masses are in a file or entered manually
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212 | YES (default) : parameters **File of masses ; Column of Id ; Number of header ; Column of masses** are visible
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213 | NO : parameter **Mass of the molecule** is visible
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214 |
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215
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216
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217 If 'use file'='YES'
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218
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219 Column of Id
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220 | Specify the column number for the id in the csv/tsv input file
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221 |
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222
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223 Number of header lines
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224 | Number of lines not containing values
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225 |
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226
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227 Column of masses
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228 | Specify the column number for the mass in the csv/tsv input file
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229 |
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230
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231 If 'use file'='NO'
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232
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233 Mass (MZ) to submit
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234 | Specify a list of mass to request
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235 | one or more mass(es) entered manually
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236 | For a masses list, writes : m1 m2 m3
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237 | You must separate yours values with space
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238 | dot (.) is for float number
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239 |
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240
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241 In all cases :
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242
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243 Delta
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244 | Tolerance of the gap in the mass
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245 | It should be between 0 and 9.0 mmu
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246
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247 Ionization
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248 | Type of ionization of the molecule : *positif, negatif, neutral*
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249 | Use neutral if query doesn't be a [M+H] or [M-H] ion
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250 | HR2 knows only the weight of uncharged molecules
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251 | so we made a correction to the masses of the value of a proton before the search
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252 | if the masses are those from a spectrometry in positive or negatif mode.
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253 | **neutral** : will do a search on the mass unchanged.
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254
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255 Initial charge
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256 | Use 0 if the molecule is not basically charged
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257
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258 Exclude some basic atom(s)
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259 List of atoms that can be exclude to the molecule : *C, N, O, H, P*
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260
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261 Golden rules
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262 | There are 7 golden rules
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263 | Some are too stringent, especially for small molecules
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264 | Use 'yes' if you want more empirical formulas
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265
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266 Add some optionnal atom(s)
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267 List of atoms that can be searched in addition to the molecule : *S, F, Cl, K, Br, Na, 13C*
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268
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269 ------------
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270 Output files
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271 ------------
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272
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273 Two types of files
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274 | hr2_VIEW.HTML : for viewing result via HTML.
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275 | hr2_TSV.tabular : for linking with others modules.
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276 | an excel-like output will be available.
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277
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278 ---------------------------------------------------
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279
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280
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281 ---------------
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282 Working example
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283 ---------------
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284
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285
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286 .. class:: warningmark
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287
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288 Refer to the corresponding "W4M HowTo" in http://workflow4metabolomics.org/howto section
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289 | Format Data For Postprocessing
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290 | Perform LCMS Annotations
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291
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292 .. class:: warningmark
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293
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294 And their "W4M courses 2018":
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295 | Using Galaxy4Metabolomics - W4M table format for Galaxy
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296 | Les banques d'annotation - Annotation
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297
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298 ]]></help>
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299 <citations>
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300 <citation type="doi">10.1186/1471-2105-8-105</citation>
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301 </citations>
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302 </tool>
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303
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