Mercurial > repos > fgiacomoni > bank_inhouse
diff bank_inhouse.xml @ 0:be582bcd6585 draft
Master branch Updating - - Fxx
| author | fgiacomoni |
|---|---|
| date | Thu, 04 Oct 2018 10:37:14 -0400 |
| parents | |
| children | 52798007c6b2 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bank_inhouse.xml Thu Oct 04 10:37:14 2018 -0400 @@ -0,0 +1,446 @@ +<tool id="bank_inhouse" name="bank_inhouse" version="1.1.3"> + <description> + search by accurate mass (and by Retention time) on a local bank + </description> + + <requirements> + <requirement type="package" version="2.90">perl-json</requirement> + <requirement type="package" version="1.97">perl-text-csv</requirement> + <requirement type="package" version="6.15">perl-lwp-simple</requirement> + <requirement type="package" version="1.74">perl-uri</requirement> + <requirement type="package" version="1.19">perl-soap-lite</requirement> + <requirement type="package" version="2.97">perl-html-template</requirement> + <requirement type="package" version="0.428">perl-list-moreutils</requirement> + <requirement type="package" version="6.15">perl-libwww-perl</requirement> + </requirements> + <stdio> + <exit_code range="1" level="fatal" /> + </stdio> + + <command><![CDATA[ + perl $__tool_directory__/bank_inhouse.pl + + #if str($input_type.choice) == "YES": + -input "${input_type.variableMetadata_in}" + #if str($input_type.header.header_choice) == "YES": + -nbheader "${input_type.header.nbheader}" + #end if + + -colmass "${input_type.colmass}" + #if str($input_type.use_file_rt.rt_file_choice) == "YES": + -colrt "${input_type.use_file_rt.colrt}" + -rt_delta "${input_type.use_file_rt.rt_file_delta}" + #end if + #else: + #if str($input_type.use_rt.rt_choice) == "YES": + -rt "${input_type.use_rt.rt}" + -rt_delta "${input_type.use_rt.rt_delta}" + #end if + -masse "${input_type.masse}" + #end if + + -mz_delta "${mz_delta_type.mz_delta}" + -mass_delta "${mz_delta_type.mass_delta}" + + #if str($bank_type.perso_bank) == "YES": + -bank_in "${bank_type.bank_in}" -bank_name "${bank_type.bank_in.name}" + -mzdb "${bank_type.mzdb}" + #if str($bank_type.bank_rt.bank_rt_choice) == "YES": + -rtdb "${bank_type.bank_rt.rtdb}" + #end if + #end if + + #if str($input_type.choice) == "YES": + -outputTab "$variableMetadata_out" + -outputXls "$bankInhouseResXls_filein" + #if str($outfiles) == "YES": + -outputFull "$variableMetadata_full_out" + #end if + #else: + -outputXls "$bankInhouseResXls_manualin" + #end if + + #if str($outfiles) == "YES": + -outputJson "$Json" + #end if + ]]></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="NO">NO</option> + <option value="YES" selected="true">YES</option> + </param> + <when value="YES"> + <param name="variableMetadata_in" type="data" label="FILE OF MASSES (format: tabular)" help="Generally variable metadata file" format="tabular" /> + + <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" 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> + + <conditional name="use_file_rt"> + <param name="rt_file_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Would you use retention time (RT)?" help="Do you have retention times in your bank? In your analyzed file? Would you use it?" /> + <when value="YES"> + <param name="colrt" label="Column of retention time (RT)" type="data_column" data_ref="variableMetadata_in" accept_default="true" /> + <param name="rt_file_delta" label="Delta of retention time (RT) (in minutes)" type="float" value="0.1" min="0" max="60" help="Default value is 0.1min"/> + </when> + <when value="NO"/> + </conditional> + + <param name="colmass" label="Column of masses (MZ)" type="data_column" data_ref="variableMetadata_in" accept_default="true" /> + </when> + <when value="NO"> + <conditional name="use_rt"> + <param name="rt_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Would you use retention time (RT)?" help="Do you have retention times in your bank? Would you use it?" /> + <when value="YES"> + <param name="rt" label="retention time (RT) to submit" type="text" size="10" help="For a rt list, writes : rt1 rt2 rt3. Your values must be separated by spaces. You should use dot (.) like decimal separator"/> + <param name="rt_delta" label="Delta of retention time (RT) (in minutes)" type="float" value="0.1" min="0" max="60" help="Default value is 0.1min"/> + </when> + <when value="NO"/> + </conditional> + + <param name="masse" type="text" label="Mass (MZ) to submit" size="20" 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> + + <conditional name="mz_delta_type"> + <param name="mz_delta" label="Delta type" type="select" display="radio" help=""> + <option value="Da">Da</option> + <option value="ppm">ppm</option> + </param> + <when value="Da"> + <param name="mass_delta" label="Delta of mass (MZ) (in Dalton)" type="float" value="0.005" min="0" max="3000" help="Default value is 0.005 Da"/> + </when> + <when value="ppm"> + <param name="mass_delta" label="Delta of mass (MZ) (in ppm)" type="float" value="5" min="0" max="300000" help="Default value is 5 ppm"/> + </when> + </conditional> + + <conditional name="bank_type"> + <param name="perso_bank" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="* Use personal data bank?" help="if 'NO' is selected an internal file will be used! It doesn't contain a retention time (RT)" /> + <when value="YES"> + <param name="bank_in" type="data" label="BANK FILE" help="" format="tabular" /> + <param name="mzdb" label="Column of masses (MZ) in Bank file" type="data_column" data_ref="bank_in" accept_default="true" /> + <conditional name="bank_rt"> + <param name="bank_rt_choice" type="boolean" checked="true" truevalue="YES" falsevalue="NO" label="Have you used the retention time (RT) for your input data?" help="Do you have retention times in your bank? In your analyzed data? Would you use it?" /> + <when value="YES"> + <param name="rtdb" label="Column of retention time (RT) in Bank file" type="data_column" data_ref="bank_in" accept_default="true" /> + </when> + <when value="NO"/> + </conditional> + </when> + <when value="NO"/> + </conditional> + <param name="outfiles" type="select" label="* Would you more output?" display="radio" help="if 'YES' is selected then 2 more files will be generate (JSON + variableMetadata and bank full column)"> + <option value="YES">YES</option> + <option value="NO" selected="true">NO</option> + </param> + </inputs> + + <outputs> + <data name="variableMetadata_out" format="tabular" label="${tool.name}_${input_type.variableMetadata_in.name}_TSV" > + <filter>(input_type['choice'] == 'YES')</filter> + </data> + <data name="bankInhouseResXls_filein" format="tabular" label="${tool.name}_${input_type.variableMetadata_in.name}_XLS" > + <filter>(input_type['choice'] == 'YES')</filter> + </data> + <data name="variableMetadata_full_out" format="tabular" label="${tool.name}_${input_type.variableMetadata_in.name}_full_TSV" > + <filter>(input_type['choice'] == 'YES')</filter> + <filter>(outfiles == 'YES')</filter> + </data> + <data name="bankInhouseResXls_manualin" format="tabular" label="${tool.name}_manual_XLS" > + <filter>(input_type['choice'] == 'NO')</filter> + </data> + <data name="Json" format="vjson" label="${tool.name}_Json" > + <filter>(outfiles == 'YES')</filter> + </data> + <!--<data name="View" format="html" label="${tool.name}_View" ></data>--> + </outputs> + + <tests> + <test> + <param name="choice" value="NO"/> + <param name="rt_choice" value="NO"/> + <param name="masse" value="422.0849114 18.0105647 535.3181236 209.987659 98.952389"/> + <param name="mz_delta" value="Da"/> + <param name="mass_delta" value="0.005"/> + <param name="perso_bank" value="NO"/> + <param name="outfiles" value="NO"/> + <output name="bankInhouseResXls_manualin" file="out_test1.tabular"/> + </test> + <test> + <param name="choice" value="YES"/> + <param name="variableMetadata_in" value="in_test2.tabular"/> + <param name="header_choice" value="YES"/> + <param name="nbheader" value="1"/> + <param name="rt_file_choice" value="NO"/> + <param name="colmass" value="2"/> + <param name="mz_delta" value="Da"/> + <param name="mass_delta" value="0.005"/> + <param name="perso_bank" value="NO"/> + <param name="outfiles" value="NO"/> + + <output name="variableMetadata_out" file="out_test2a.tabular"/> + <output name="bankInhouseResXls_filein" file="out_test2b.tabular"/> + </test> + <!-- + <test> + <param name="choice" value="YES"/> + <param name="variableMetadata_in" value="in_test3.tabular"/> + <param name="header_choice" value="YES"/> + <param name="nbheader" value="1"/> + <param name="rt_file_choice" value="NO"/> + <param name="colmass" value="2"/> + <param name="mz_delta" value="Da"/> + <param name="mass_delta" value="0.005"/> + <param name="perso_bank" value="NO"/> + <param name="outfiles" value="NO"/> + + <output name="variableMetadata_out" file="out_test3a.tabular"/> + <output name="bankInhouseResXls_filein" file="out_test3b.tabular"/> + </test> + <test> + <param name="choice" value="YES"/> + <param name="variableMetadata_in" value="in_test4.tabular"/> + <param name="header_choice" value="YES"/> + <param name="nbheader" value="1"/> + <param name="rt_file_choice" value="YES"/> + <param name="colrt" value="10"/> + <param name="rt_file_delta" value="0.2"/> + <param name="colmass" value="8"/> + <param name="mz_delta" value="Da"/> + <param name="mass_delta" value="0"/> + <param name="perso_bank" value="YES"/> + <param name="bank_in" value="in_test4.tabular"/> + <param name="mzdb" value="8"/> + <param name="bank_rt_choice" value="YES"/> + <param name="rtdb" value="10"/> + <param name="outfiles" value="YES"/> + + <output name="variableMetadata_out" file="out_test4a.tabular"/> + <output name="bankInhouseResXls_filein" file="out_test4b.tabular"/> + <output name="variableMetadata_full_out" file="out_test4c.tabular"/> + <output name="Json" file="out_test4d.vjson"/> + </test>--> + </tests> + + <help><![CDATA[ + +.. class:: infomark + +**Authors** + | Marion Landi - FLAME ; PFEM ; INRA ; MetaboHUB (for original version and development of this Perl script and for xml interface and Perl wrapper) + +--------------------------------------------------- + + +============== +bank_inhouse +============== + +----------- +Description +----------- + + | Search informations on a local bank with one or more mass(es), with or without retention time, in a file or entered manually + + +Keywords +======== + +Masses + rt to inhouse info + + +----------------- +Workflow position +----------------- + + +.. image:: bank_inhouse.png + :width: 800 + + +----------- +Input files +----------- + + ++-----------------------------+-----------+ +| Parameter : num + label | Format | ++=============================+===========+ +| 1 : File of masses | tabular | ++-----------------------------+-----------+ +| 2 : personal data bank file | tabular | ++-----------------------------+-----------+ + +File of masses (Generally variable metadata file) must have at least the 2 following column : + | Id : column to identify masses in the tsv input file + | Masses : column with all the masses in the tsv input file + | RT : (optional) column with all the retention time in the tsv input file + | + +personal data bank file must contain certain columns : + | Masses (Mandatory) and RT (optional) + | + +---------- +Parameters +---------- + +Would you use a file + | Choose whether the masses are in a file or entered manually + | YES (default) : parameters **File of masses ; Do you have a header ; Column of Id ; Column of masses** are visible + | NO : parameter **Mass to submit** is visible + | + + +If 'use file'='YES' + +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 Id + | Specify the column number for the id in the tsv input file + | + +Would you use retention time (RT) + | YES (default) : parameter **Column of retention time (RT)** and **Delta of retention time (RT) (in minutes)** are visible + | NO : Search will be made solely on the basis of the masses + | + +If 'Would you use retention time (RT)'='YES' + +Column of retention time (RT) + | Specify the column number for the retention time (RT) in the tsv input file + | + +Delta of retention time (RT) (in minutes) + | Specify a delta to apply on retention time - This value is a float. + | + +In all RT cases : + +Column of masses + | Specify the column number for the mass in the tsv input file + | + + +If 'use file'='NO' + +Would you use retention time (RT) + | YES (default) : parameter **retention time (RT) to submit** and **Delta of retention time (RT) (in minutes)** are visible + | NO : Search will be made solely on the basis of the masses + | + +If 'Would you use retention time (RT)'='YES' + +retention time (RT) to submit + | Specify a list of retention time to request + | one or more retention time entered manually + | For a RT list, writes : rt1 rt2 rt3 + | You must separate yours values with space + | dot (.) is for float number + | +Delta of retention time (RT) (in minutes) + | Specify a delta to apply on retention time - This value is a float. + | + +In all RT cases : + +Mass 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 type + | Specify a delta type : "in Dalton" or "in ppm" + | + +Delta of mass ("in Dalton" or "in ppm" according to choice) + | Specify a delta to apply on mass - This value is a float. + | + +Use personal data bank + | YES : parameter **Bank file**, **Column of masses (MZ) in Bank file** and **Column of retention time (RT) in Bank file** (optional) are visible, the search will be made only on the information of the file + | NO : a internal bank will be used + | + +If 'Use personal data bank'='YES' + +Bank file + | see "Input files" section above + | Tabular file format, Generally variable metadata file + | + +Column of masses + | Specify the column number for the mass in the bank input file + | + +Have you used the retention time (RT) for your input data + | Answering same as for "Would you use retention time (RT)" + | YES (default) : parameter **Column of retention time (RT) in Bank file** is visible + | NO : Search will be made solely on the basis of the masses + | + +Column of retention time (RT) in Bank file + | Specify the column number for the rt in the bank input file + | + + +------------ +Output files +------------ + +Two types of files (if you manually enter the masses both files are mingled): + | bank_inhouse_(input.name)_TSV.tabular : for linking with others modules. + | + | bank_inhouse_(input.name)_XLS.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 2016": + | Using Galaxy4Metabolomics - W4M table format for Galaxy + | Annotation Banks - Annotation + + ]]></help> +</tool>