Mercurial > repos > fgiacomoni > bank_inhouse
view bank_inhouse.xml @ 0:be582bcd6585 draft
Master branch Updating - - Fxx
author | fgiacomoni |
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date | Thu, 04 Oct 2018 10:37:14 -0400 |
parents | |
children | 52798007c6b2 |
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<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>