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1 <tool id="bih4maconda" name="Bih4MaConDa" version="0.1.3">
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2 <description>
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3 : Utility to detect potential contaminants in your peak list based on MaConDa database
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="0.2.0">perl-metabolomics-fragment-annotation</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1" level="fatal" />
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10 </stdio>
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11
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12 <command><![CDATA[
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13 perl $__tool_directory__/bih4maconda.pl
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14 -input $variableMetadata_in
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15 -mzCol $colmass
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16
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17 #if str($has_header.header_choice) == "YES":
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18 -header "${has_header.header}"
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19 #end if
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20
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21 -ppmError $ppm_error
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22 -mode $mode
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23 -outputTab $outputTab
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24 -outputFull $outFull
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25 -verbose $verbose
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26 ]]></command>
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27 <inputs>
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28 <param name="variableMetadata_in" type="data" label="Input file containing a list of mzs (format: tabular)" help="Generally variable metadata file" format="tabular" />
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29
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30 <conditional name="has_header">
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31 <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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32 <when value="YES">
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33 <param name="header" type="integer" label="Number of header lines" value="1" min="1" max="10" help="number of lines not containing masses"/>
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34 </when>
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35 <when value="NO"/>
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36 </conditional>
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37
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38 <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" />
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39
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40 <param name="verbose" type="select" label="Verbose level" display="radio" help="">
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41 <option value="1" selected="true">Low</option>
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42 <option value="3" >High</option>
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43 </param>
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44
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45
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46 <param name="ppm_error" label="Tolerance in ppm used during annotation step" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/>
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47
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48 <param name="mode" label="Molecular Species " type="select" display="radio" help="">
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49 <option value="POSITIVE">Positif Mode</option>
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50 <option value="NEGATIVE">Negatif Mode</option>
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51 <option value="NEUTRAL">Neutral Mass</option>
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52 </param>
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53
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54 </inputs>
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55 <outputs>
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56 <data name="outFull" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA_Full.tabular" />
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57 <data name="outputTab" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA.tabular" />
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58 </outputs>
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59
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60 <help><![CDATA[
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61
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62 .. class:: infomark
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63
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64 **Authors**
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65 | Franck Giacomoni - FLAME ; PFEM ; INRA ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper)
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66
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67 ---------------------------------------------------
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68
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69
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70 ======================
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71 bih4MaDonDa
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72 ======================
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73
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74 -----------
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75 Description
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76 -----------
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77
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78 | detection of potential contaminants in your peak list based on MaConDa database
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79
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80
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81 Keywords
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82 ========
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83
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84 contaminants
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85
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86
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87 -----------------
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88 Workflow position
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89 -----------------
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90
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91
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92 .. image::
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93 :width: 800
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94
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95
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96 -----------
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97 Input files
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98 -----------
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99
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100
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101 +--------------------------------+-----------+
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102 | Parameter : num + label | Format |
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103 +================================+===========+
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104 | 1 : File with a list of masses | tabular |
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105 +--------------------------------+-----------+
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106
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107 File of masses (Generally variable metadata file) must have at least the following column :
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108 | Masses : column with all the masses in the tabular input file
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109 |
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110
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111
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112 ----------
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113 Parameters
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114 ----------
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115
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116 File of masses
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117 | see "Input files" section above
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118 | Tabular file format, Generally variable metadata file
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119 |
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120
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121 Do you have a header
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122 | YES (default) : parameter **Number of header lines** is visible
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123 | NO : all lines are considered to contain masses
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124 |
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125
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126 If 'have a header'='YES'
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127
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128 Number of header lines
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129 | Number of lines not containing masses values, these lines will be ignored
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130 |
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131
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132 In all header cases :
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133
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134 Column of Masses
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135 | Specify the column number for the mz in the tabular input file
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136 |
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137
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138
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139 In all cases :
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140
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141 PPM error
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142 | Specify a delta (in ppm) to apply on annotating mass - This value is a float.
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143 |
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144
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145
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146 ------------
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147 Output files
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148 ------------
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149
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150 Two types of files (if you manually enter the masses both files are mingled):
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151 | BIH4MACONDA_(input.name)_FULL.tabular : for linking with others modules.
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152 | BIH4MACONDA_(input.name).tabular : an excel-like output will be available.
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153 |
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154
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155
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156 ---------------------------------------------------
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157
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158 ---------------
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159 Working example
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160 ---------------
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161
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162
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163 .. class:: warningmark
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164
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165 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto
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166 | Format Data For Postprocessing
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167 | Perform LCMS Annotations
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168
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169 .. class:: warningmark
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170
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171 And their "W4M courses 2018":
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172 | Using Galaxy4Metabolomics - W4M table format for Galaxy
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173 | Annotation Banks - Annotation
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174
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175 ]]></help>
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176 <citations>
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177 <citation type="doi">10.1093/bioinformatics/bts527</citation>
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178 </citations>
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179 </tool> |
