Mercurial > repos > fgiacomoni > hr2
diff HR2.xml @ 0:86296c048e46 draft
Init repository for [hr2]
author | fgiacomoni |
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date | Wed, 05 Jun 2019 09:40:20 -0400 |
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children | e2cbcf6fa22e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/HR2.xml Wed Jun 05 09:40:20 2019 -0400 @@ -0,0 +1,303 @@ +<tool id="hr2" name="HR2 formula" version="1.1.1.7"> + <description> + find a chemical formula from a accurate mass + </description> + <requirements> + <requirement type="package" version="2.161">perl-data-dumper</requirement> + <requirement type="package" version="1.97">perl-text-csv</requirement> + <requirement type="package" version="2.97">perl-html-template</requirement> + <requirement type="package" version="1.04">hr2</requirement> + </requirements> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + + + <command><![CDATA[ + perl $__tool_directory__/hr2_manager.pl + #if str($input_type.choice) == "YES": + -input "${input_type.input}" + #if str($input_type.header.header_choice) == "yes": + -nblineheader "${$input_type.header.nbHeader}" + #end if + -colId "${input_type.colId}" -colmass "${input_type.colmass}" + #else: + -masse "${input_type.masse}" + #end if + + -tolerance "$tol" + -mode "${mode_condition.mode}" + #if str($mode_condition.mode) == "neutral": + -charge "0" + #else: + -charge "${mode_condition.qtCharge}" + #end if + + -regleOr "$regleOr" -atomes "$atomes_basic" -atomessup "$atomes_sup" + -output1 "$variableMetadata" -outputView "$hr2ResView" + -verbose "$verbose" + ]]></command> + + <inputs> + <conditional name="input_type"> + <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"> + <option value="YES">YES</option> + <option value="NO">NO</option> + </param> + <when value="YES"> + <param name="input" label="File of masses" format="tabular" type="data" /> + <conditional name="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="nbHeader" label="Number of header lines" type="integer" value="1" min="1" size="10" help="number of lines not containing masses"/> + </when> + <when value="no"/> + </conditional> + <param name="colId" label="Column of Id" type="data_column" data_ref="input" accept_default="true" /> + <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="input" accept_default="true" /> + </when> + <when value="NO"> + <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"/> + </when> + </conditional> + + <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"/> + <conditional name="mode_condition"> + <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"> + <option value="positive">positive</option> + <option value="negative">negative</option> + <option value="neutral" selected="true">neutral</option> + </param> + <when value="neutral"/> + <when value="positive"> + <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged"> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + </param> + </when> + <when value="negative"> + <param name="qtCharge" label="Molecule initial charge" type="select" help="Use 'neutral' if the molecule is not charged"> + <option value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + </param> + </when> + </conditional> + <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"> + <option value="C" selected="true">C</option> + <option value="N" selected="true">N</option> + <option value="O" selected="true">O</option> + <option value="H" selected="true">H</option> + <option value="P" selected="true">P</option> + </param> + <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"> + <option value="YES">only first 3 rules</option> + <option value="NO" selected="true">all 7 rules</option> + </param> + <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"> + <option value="S">S</option> + <option value="F">F</option> + <option value="L">Cl</option> + <option value="K">K</option> + <option value="B">Br</option> + <option value="A">Na</option> + <option value="1">13C</option> + </param> + <param name="verbose" type="select" label="Verbose level" display="radio" help=""> + <option value="1" selected="true">Low</option> + <option value="3" >High</option> + </param> + </inputs> + <outputs> + <data name="variableMetadata" format="tabular" label="${tool.name}_TSV"/> + <data name="hr2ResView" format="html" label="${tool.name}_VIEW"/> + </outputs> + + <tests> + <test> + <param name="choice" value="NO"/> + <param name="masse" value="175.125"/> + <param name="tolerance" value="1.0"/> + <param name="mode" value="negative"/> + <param name="qtCharge" value="1"/> + <param name="atomes_basic" value="C,O,N,H"/> + <param name="regleOr" value="NO"/> + <param name="verbose" value="3"/> + <output name="variableMetadata" file="out_test01.tabular"/> + <output name="hr2ResView" file="out_test01.html"/> + </test> + <test> + <param name="choice" value="NO"/> + <param name="masse" value="88.052"/> + <param name="tolerance" value="1.0"/> + <param name="mode" value="neutral"/> + <param name="qtCharge" value="1"/> + <param name="atomes_basic" value="C,O,H"/> + <param name="regleOr" value="NO"/> + <param name="verbose" value="3"/> + <output name="variableMetadata" file="out_test02.tabular"/> + <output name="hr2ResView" file="out_test02.html"/> + </test> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +**Authors** + | HR2 original program and its documentation are Copyright (c) 1992-2005 by Joerg Hau under GNU General Public License ("GPL") + +.. class:: infomark + +**Wrapping** + | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for xml interface and Perl wrapper) + | Franck Giacomoni - PFEM ; INRA ; MetaboHUB (for xml interface, conda dependancies and Perl wrapper) + +--------------------------------------------------- + +.. class:: infomark + +**Please cite** If you use this tool, please cite + | 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 + | 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 + + +--------------------------------------------------- + +============== +HR2 formula +============== + +----------- +Description +----------- + + | Find a formula for the masses + | only molecules with carbon (C) will be search + + +----------------- +Workflow position +----------------- + + +.. image:: ./static/images/metabolomics/hr2.png + :width: 800 + + + + +----------- +Input files +----------- + ++-------------------------+-----------+ +| Parameter : num + label | Format | ++=========================+===========+ +| 1 : variableMetadata | tabular | ++-------------------------+-----------+ + +File variableMetadata must have at least the 2 following columns : + * Id : column to identify masses in the csv/tsv input file + * Masses : column with all the masses in the csv/tsv input file + + +---------- +Parameters +---------- + +Would you use a file + | Choose whether the masses are in a file or entered manually + | YES (default) : parameters **File of masses ; Column of Id ; Number of header ; Column of masses** are visible + | NO : parameter **Mass of the molecule** is visible + | + + +If 'use file'='YES' + +Column of Id + | Specify the column number for the id in the csv/tsv input file + | + +Number of header lines + | Number of lines not containing values + | + +Column of masses + | Specify the column number for the mass in the csv/tsv input file + | + +If 'use file'='NO' + +Mass (MZ) to submit + | Specify a list of mass to request + | one or more mass(es) entered manually + | For a masses list, writes : m1 m2 m3 + | You must separate yours values with space + | dot (.) is for float number + | + +In all cases : + +Delta + | Tolerance of the gap in the mass + | It should be between 0 and 9.0 mmu + +Ionization + | Type of ionization of the molecule : *positif, negatif, neutral* + | Use neutral if query doesn't be a [M+H] or [M-H] ion + | HR2 knows only the weight of uncharged molecules + | so we made a correction to the masses of the value of a proton before the search + | if the masses are those from a spectrometry in positive or negatif mode. + | **neutral** : will do a search on the mass unchanged. + +Initial charge + | Use 0 if the molecule is not basically charged + +Exclude some basic atom(s) + List of atoms that can be exclude to the molecule : *C, N, O, H, P* + +Golden rules + | There are 7 golden rules + | Some are too stringent, especially for small molecules + | Use 'yes' if you want more empirical formulas + +Add some optionnal atom(s) + List of atoms that can be searched in addition to the molecule : *S, F, Cl, K, Br, Na, 13C* + +------------ +Output files +------------ + +Two types of files + | hr2_VIEW.HTML : for viewing result via HTML. + | hr2_TSV.tabular : for linking with others modules. + | an excel-like output will be available. + +--------------------------------------------------- + + +--------------- +Working example +--------------- + + +.. class:: warningmark + +Refer to the corresponding "W4M HowTo" in http://workflow4metabolomics.org/howto section + | Format Data For Postprocessing + | Perform LCMS Annotations + +.. class:: warningmark + +And their "W4M courses 2018": + | Using Galaxy4Metabolomics - W4M table format for Galaxy + | Les banques d'annotation - Annotation + + ]]></help> + <citations> + <citation type="doi">10.1186/1471-2105-8-105</citation> + </citations> +</tool> +