view assess_purity_msms.xml @ 28:fa5838760aee draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 1800a3818988f21ef129e500818c9a087fce5875

<tool id="assess_purity_msms" name="assess_purity_msms" version="0.0.9">
    <description>
        Assess the precursor ion purity for fragmentation spectra acquired from either a LC-MS/MS or DI-MS/MS (MSn) experiment
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />


 <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript"><![CDATA[
        assess_purity_msms.R
            --out_dir=.
            #if $mzML_data.format == "mzML_files"
                --mzML_files='
                #for $i in $mzML_data.source
                    $i,
                #end for
                '
                --galaxy_names='
                #for $i in $mzML_data.source
                    $i.name,
                #end for
                '
            #elif $mzML_data.format == "library"
                --mzML_files $__app__.config.user_library_import_dir/$__user_email__/$mzML_data.source
            #end if
                    #if $offsets.offsets == 'user'
                --minOffset=$minoffset
                --maxOffset=$maxoffset
            #end if

            --iwNorm=$iw_norm
            --ilim=$ilim

            --cores=\${GALAXY_SLOTS:-4}

            #if $nearest
                --nearest
            #end if

            #if $mostIntense
                --mostIntense
            #end if

            #if $isotopes.isotopes == "exclude_default"
                --exclude_isotopes
            #elif $isotopes.isotopes == "user"
                --exclude_isotopes
                --isotope_matrix=$isotopes.im
            #end if

    ]]></command>
    <inputs>

        <conditional name="mzML_data">
            <param name="format" type="select" label="Choose the source for the dataset" >
                <option value="mzML_files" selected="true">.mzML files to check purity from</option>
                <option value="library">Library directory name (to be used with dimspy workflows) or path to
                                        to an individual .mzML file</option>
            </param>
            <when value="mzML_files">
                <param name="source" type="data_collection" format="mzml" label="*.mzML files" >
                    <validator type="empty_field" />
                </param>
            </when>
            <when value="library">
                <param name="source" type="text"
                       size="40" label="Library directory containing *.mzml files
                                                                 or path to an individual *.mzML">
                    <validator type="empty_field" />
                </param>
            </when>
        </conditional>

         <param name="mostIntense" type="boolean" checked="true" label="Use most intense peak within isolation window for precursor?"
               help="If yes, this will ignore the recorded precursor within the mzML file and use
               use the most intense peak within the isolation window to calculate the precursor ion purity"/>

        <param name="nearest" type="boolean" checked="true" label="Use nearest full scan to determine precursor?"
               help="If yes, this will use the neareset full scan to the fragmentation scan to determine what the m/z value
                     is of the precursor"/>


        <conditional name="offsets">
            <param name="offsets" type="select" label="offsets" >
                <option value="auto" selected="true">Uses offsets determined in the mzML file</option>
                <option value="user">User supplied offset values</option>
            </param>
            <when value="user">
                <expand macro="offsets" />
            </when>
	        <when value="auto">
            </when>

        </conditional>

        <expand macro="general_params" />


    </inputs>
    <outputs>
	    <data name="assess_purity_msms" format="tsv" label="${tool.name} on ${on_string}: tsv"
              from_work_dir="purity_msms.tsv" />
        <data name="assess_purity_msms_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
              from_work_dir="purity_msms.RData" />
    </outputs>
    <tests>
       <test>
        <conditional name="mzML_data">
           <param name="format" value="mzML_files"/>
           <param name="source" >
                <collection type="list">
                    <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
                </collection>
            </param>
        </conditional>
        <output name="assess_purity_msms" value="assess_purity_msms_output_LCMSMS1.tsv" />
        </test>
    </tests>
    
    <help><![CDATA[
=============================================================
Assess precursor ion purity of MS/MS files
=============================================================
-----------
Description
-----------

Tool to assess precursor ion purity of MS/MS files

Data input of mzML files either from:

* A data collection of the mzML files containing MS/MS scans
* A path to a folder that has mzML files containing MS/MS scans

See Bioconductor documentation for more details about the function used, msPurity::purityA().

-----------
Outputs
-----------

* purity_msms: A tsv file of all the precursor ion purity score (and other metrics) of each fragmentation spectra
* purity_msms_rdata: The purityA object saved as an rdata file


    ]]></help>
<expand macro="citations" />
</tool>