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annotate bih4maconda.xml @ 1:2744d20c830a draft default tip
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| author | fgiacomoni |
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| date | Fri, 27 Nov 2020 11:21:58 +0000 |
| parents | de13e2c45971 |
| children |
| rev | line source |
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1 <tool id="bih4maconda" name="Bih4MaConDa" version="0.1.4"> |
| 0 | 2 <description> |
| 3 : Utility to detect potential contaminants in your peak list based on MaConDa database | |
| 4 </description> | |
| 5 <requirements> | |
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6 <requirement type="package" version="0.6.3">perl-metabolomics-fragment-annotation</requirement> |
| 0 | 7 </requirements> |
| 8 <stdio> | |
| 9 <exit_code range="1" level="fatal" /> | |
| 10 </stdio> | |
| 11 | |
| 12 <command><![CDATA[ | |
| 13 perl $__tool_directory__/bih4maconda.pl | |
| 14 -input $variableMetadata_in | |
| 15 -mzCol $colmass | |
| 16 | |
| 17 #if str($has_header.header_choice) == "YES": | |
| 18 -header "${has_header.header}" | |
| 19 #end if | |
| 20 | |
| 21 -ppmError $ppm_error | |
| 22 -mode $mode | |
| 23 -outputTab $outputTab | |
| 24 -outputFull $outFull | |
| 25 -verbose $verbose | |
| 26 ]]></command> | |
| 27 <inputs> | |
| 28 <param name="variableMetadata_in" type="data" label="Input file containing a list of mzs (format: tabular)" help="Generally variable metadata file" format="tabular" /> | |
| 29 | |
| 30 <conditional name="has_header"> | |
| 31 <param name="header_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Do you have a header?" help="if 'YES' is selected then enter your number of header lines" /> | |
| 32 <when value="YES"> | |
| 33 <param name="header" type="integer" label="Number of header lines" value="1" min="1" max="10" help="number of lines not containing masses"/> | |
| 34 </when> | |
| 35 <when value="NO"/> | |
| 36 </conditional> | |
| 37 | |
| 38 <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" /> | |
| 39 | |
| 40 <param name="verbose" type="select" label="Verbose level" display="radio" help=""> | |
| 41 <option value="1" selected="true">Low</option> | |
| 42 <option value="3" >High</option> | |
| 43 </param> | |
| 44 | |
| 45 | |
| 46 <param name="ppm_error" label="Tolerance in ppm used during annotation step" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/> | |
| 47 | |
| 48 <param name="mode" label="Molecular Species " type="select" display="radio" help=""> | |
| 49 <option value="POSITIVE">Positif Mode</option> | |
| 50 <option value="NEGATIVE">Negatif Mode</option> | |
| 51 <option value="NEUTRAL">Neutral Mass</option> | |
| 52 </param> | |
| 53 | |
| 54 </inputs> | |
| 55 <outputs> | |
| 56 <data name="outFull" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA_Full.tabular" /> | |
| 57 <data name="outputTab" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA.tabular" /> | |
| 58 </outputs> | |
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59 <tests> |
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60 <!--test 01 : short input id, mz and rt data --> |
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61 <test> |
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62 <param name="variableMetadata_in" value="in_test01_pos.tabular"/> |
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63 <param name="header_choice" value="YES"/> |
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64 <param name="header" value="1"/> |
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65 <param name="colmass" value="2"/> |
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66 <param name="ppm_error" value="5"/> |
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67 <param name="mode" value="POSITIVE"/> |
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68 <param name="verbose" value="3"/> |
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69 <output name="outFull" file="outFull_test01.tabular"/> |
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70 <output name="outputTab" file="outTab_test01.tabular"/> |
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71 </test> |
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72 </tests> |
| 0 | 73 <help><![CDATA[ |
| 74 | |
| 75 .. class:: infomark | |
| 76 | |
| 77 **Authors** | |
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78 | Franck Giacomoni - FLAME ; PFEM ; INRA ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper) - based on the Perl CPAN package Metabolomics::Fragmentation::Annotation |
| 0 | 79 |
| 80 --------------------------------------------------- | |
| 81 | |
| 82 | |
| 83 ====================== | |
| 84 bih4MaDonDa | |
| 85 ====================== | |
| 86 | |
| 87 ----------- | |
| 88 Description | |
| 89 ----------- | |
| 90 | |
| 91 | detection of potential contaminants in your peak list based on MaConDa database | |
| 92 | |
| 93 | |
| 94 Keywords | |
| 95 ======== | |
| 96 | |
| 97 contaminants | |
| 98 | |
| 99 | |
| 100 ----------------- | |
| 101 Workflow position | |
| 102 ----------------- | |
| 103 | |
| 104 | |
| 105 .. image:: | |
| 106 :width: 800 | |
| 107 | |
| 108 | |
| 109 ----------- | |
| 110 Input files | |
| 111 ----------- | |
| 112 | |
| 113 | |
| 114 +--------------------------------+-----------+ | |
| 115 | Parameter : num + label | Format | | |
| 116 +================================+===========+ | |
| 117 | 1 : File with a list of masses | tabular | | |
| 118 +--------------------------------+-----------+ | |
| 119 | |
| 120 File of masses (Generally variable metadata file) must have at least the following column : | |
| 121 | Masses : column with all the masses in the tabular input file | |
| 122 | | |
| 123 | |
| 124 | |
| 125 ---------- | |
| 126 Parameters | |
| 127 ---------- | |
| 128 | |
| 129 File of masses | |
| 130 | see "Input files" section above | |
| 131 | Tabular file format, Generally variable metadata file | |
| 132 | | |
| 133 | |
| 134 Do you have a header | |
| 135 | YES (default) : parameter **Number of header lines** is visible | |
| 136 | NO : all lines are considered to contain masses | |
| 137 | | |
| 138 | |
| 139 If 'have a header'='YES' | |
| 140 | |
| 141 Number of header lines | |
| 142 | Number of lines not containing masses values, these lines will be ignored | |
| 143 | | |
| 144 | |
| 145 In all header cases : | |
| 146 | |
| 147 Column of Masses | |
| 148 | Specify the column number for the mz in the tabular input file | |
| 149 | | |
| 150 | |
| 151 | |
| 152 In all cases : | |
| 153 | |
| 154 PPM error | |
| 155 | Specify a delta (in ppm) to apply on annotating mass - This value is a float. | |
| 156 | | |
| 157 | |
| 158 | |
| 159 ------------ | |
| 160 Output files | |
| 161 ------------ | |
| 162 | |
| 163 Two types of files (if you manually enter the masses both files are mingled): | |
| 164 | BIH4MACONDA_(input.name)_FULL.tabular : for linking with others modules. | |
| 165 | BIH4MACONDA_(input.name).tabular : an excel-like output will be available. | |
| 166 | | |
| 167 | |
| 168 | |
| 169 --------------------------------------------------- | |
| 170 | |
| 171 --------------- | |
| 172 Working example | |
| 173 --------------- | |
| 174 | |
| 175 | |
| 176 .. class:: warningmark | |
| 177 | |
| 178 Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto | |
| 179 | Format Data For Postprocessing | |
| 180 | Perform LCMS Annotations | |
| 181 | |
| 182 .. class:: warningmark | |
| 183 | |
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184 And their "W4M courses 2019": |
| 0 | 185 | Using Galaxy4Metabolomics - W4M table format for Galaxy |
| 186 | Annotation Banks - Annotation | |
| 187 | |
| 188 ]]></help> | |
| 189 <citations> | |
| 190 <citation type="doi">10.1093/bioinformatics/bts527</citation> | |
| 191 </citations> | |
| 192 </tool> |