Mercurial > repos > fgiacomoni > bih4maconda
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Init repository for bih4maconda
author | fgiacomoni |
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date | Tue, 21 Jan 2020 15:49:00 -0500 |
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children | 2744d20c830a |
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<tool id="bih4maconda" name="Bih4MaConDa" version="0.1.3"> <description> : Utility to detect potential contaminants in your peak list based on MaConDa database </description> <requirements> <requirement type="package" version="0.2.0">perl-metabolomics-fragment-annotation</requirement> </requirements> <stdio> <exit_code range="1" level="fatal" /> </stdio> <command><![CDATA[ perl $__tool_directory__/bih4maconda.pl -input $variableMetadata_in -mzCol $colmass #if str($has_header.header_choice) == "YES": -header "${has_header.header}" #end if -ppmError $ppm_error -mode $mode -outputTab $outputTab -outputFull $outFull -verbose $verbose ]]></command> <inputs> <param name="variableMetadata_in" type="data" label="Input file containing a list of mzs (format: tabular)" help="Generally variable metadata file" format="tabular" /> <conditional name="has_header"> <param name="header_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Do you have a header?" help="if 'YES' is selected then enter your number of header lines" /> <when value="YES"> <param name="header" type="integer" label="Number of header lines" value="1" min="1" max="10" help="number of lines not containing masses"/> </when> <when value="NO"/> </conditional> <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" /> <param name="verbose" type="select" label="Verbose level" display="radio" help=""> <option value="1" selected="true">Low</option> <option value="3" >High</option> </param> <param name="ppm_error" label="Tolerance in ppm used during annotation step" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/> <param name="mode" label="Molecular Species " type="select" display="radio" help=""> <option value="POSITIVE">Positif Mode</option> <option value="NEGATIVE">Negatif Mode</option> <option value="NEUTRAL">Neutral Mass</option> </param> </inputs> <outputs> <data name="outFull" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA_Full.tabular" /> <data name="outputTab" format="tabular" label="${variableMetadata_in.name[:-6]}.BIH4MACONDA.tabular" /> </outputs> <help><![CDATA[ .. class:: infomark **Authors** | Franck Giacomoni - FLAME ; PFEM ; INRA ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper) --------------------------------------------------- ====================== bih4MaDonDa ====================== ----------- Description ----------- | detection of potential contaminants in your peak list based on MaConDa database Keywords ======== contaminants ----------------- Workflow position ----------------- .. image:: :width: 800 ----------- Input files ----------- +--------------------------------+-----------+ | Parameter : num + label | Format | +================================+===========+ | 1 : File with a list of masses | tabular | +--------------------------------+-----------+ File of masses (Generally variable metadata file) must have at least the following column : | Masses : column with all the masses in the tabular input file | ---------- Parameters ---------- File of masses | see "Input files" section above | Tabular file format, Generally variable metadata file | Do you have a header | YES (default) : parameter **Number of header lines** is visible | NO : all lines are considered to contain masses | If 'have a header'='YES' Number of header lines | Number of lines not containing masses values, these lines will be ignored | In all header cases : Column of Masses | Specify the column number for the mz in the tabular input file | In all cases : PPM error | Specify a delta (in ppm) to apply on annotating mass - This value is a float. | ------------ Output files ------------ Two types of files (if you manually enter the masses both files are mingled): | BIH4MACONDA_(input.name)_FULL.tabular : for linking with others modules. | BIH4MACONDA_(input.name).tabular : an excel-like output will be available. | --------------------------------------------------- --------------- Working example --------------- .. class:: warningmark Refer to the corresponding W4M HowTo section: http://workflow4metabolomics.org/howto | Format Data For Postprocessing | Perform LCMS Annotations .. class:: warningmark And their "W4M courses 2018": | Using Galaxy4Metabolomics - W4M table format for Galaxy | Annotation Banks - Annotation ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/bts527</citation> </citations> </tool>