<tool id="mspurity_purityx" name="msPurity.purityX" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
        <description>Calculate the anticipated precursor ion purity from a LC-MS XCMS dataset.
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/purityX.R'
            --xset_path='$xset'
            --out_dir='.'
            --minOffset=$minoffset
            --maxOffset=$maxoffset
            --singleFile=$singleFile
            --purityType=$purityType
            --cores=\${GALAXY_SLOTS:-4}
            #if $xgroups.xgroups == "choose"
                --xgroups='$xgroups.xgroups_value'
            #end if
            --camera_xcms=$camera_xcms

            --iwNorm=$iw_norm
            --ilim=$ilim
            #if $isotopes.isotopes == "exclude_default"
                --exclude_isotopes
            #elif $isotopes.isotopes == "user"
                --exclude_isotopes
                --isotope_matrix='$isotopes.im'
            #end if
            #if $file_load_conditional.file_load_select == 'yes'
                --galaxy_files='
                #for $i in $file_load_conditional.input
                    $i,
                #end for
                '
            #end if
            #if $file_load_conditional.file_load_select == 'yes'
                --files='
                #for $i in $file_load_conditional.input
                    $i.name,
                #end for
                '
            #end if

            #if $choose_class_cond.choose_class== 'choose'
                --choose_class=$choose_class_cond.class
            #end if
            #if $ignore_files_cond.ignore_files_choice== 'choose'
                --ignore_files=$ignore_files_cond.ignore_files
            #end if

            #if $raw_rt_columns
                --rtraw_columns
            #end if


    ]]></command>
    <inputs>

        <param argument="--xset" type="data" format="rdata"
                help="xcmsSet object saved as an RData file"/>
        <expand macro="offsets" />
        <expand macro="general_params" />
        <param argument="--singleFile" type="integer" label="singleFile" value="0"
                    help="If just a single file for purity is to be calculated (rather than the grouped XCMS peaks).
                    Uses the index of the files in xcmsSet object. If zero this is ignored"/>

        <conditional name="choose_class_cond">
            <param name="choose_class" type="select" label="Choose class of XCMS set object to perform calculation on?" >
                <option value="choose">Choose class</option>
                <option value="all" selected="true">calculate average across all classes</option>
            </param>
            <when value="all">
            </when>
            <when value="choose">
                <param argument="--class" type="text" label="Choose class"
                    help="Comma separated string of classes (found in the phenoData slot of xcmsSet object
                    i.e. xset@phenoData). An average will across all the choosen classes." />
            </when>
        </conditional>

        <conditional name="ignore_files_cond">
            <param name="ignore_files_choice" type="select" label="Ignore files?" >
                <option value="choose">Choose files to ignore from calculation</option>
                <option value="none" selected="true" >Include all files of selected classes in calculation</option>
            </param>
            <when value="none">
            </when>
            <when value="choose">
               <param argument="--ignore_files" type="text" label="ignore files"
               help="Comma separated string of filenames to ignore (do not include the directory) eg. blank1.mzML,blank2.mzML,sample4.mzML"  />
            </when>
        </conditional>


        <conditional name="xgroups">
            <param name="xgroups" type="select" label="xgroups" >
                <option value="choose">Choose XCMS grouped features to calculate precursor ion purity</option>
                <option value="all" selected="true">Calculate precursor ion purity for all XCMS grouped features</option>
            </param>
            <when value="choose">
                <param name="xgroups_value" type="text" label="xgroup ids"
                    help="Comma separated string of xcms groups to perform prediction on eg. 1,2,3,4"  />
            </when>
            <when value="all"/>
        </conditional>


        <param argument="--purityType" type="select" label="Method of averaging purity"
               help="Area and average used for the purity predictions. FWHM='Full width half maximum', FW='Full width'">
                <option value="purityFWHMmedian" selected="true" >FWHM median</option>
                <option value="purityFWHMmean" >FWHM mean</option>
                <option value="purityFWmedian" >FW median</option>
                <option value="purityFWmean" >FW mean</option>
        </param>

        <expand macro="camera_xcms" />

        <param argument="--raw_rt_columns" type="boolean" label="Has the raw retention time been tracked within the peaks?"
               help="[Deprecated] No longer applicable. Previously when obiwarp was used
                     the retention time correction tracking was slightly different to the other correction methods. To ensure
                     correct tracking with obiwarp an additional tool (track_rt_raw) was performed prior to
                     any retention time correction - and this was then checked when this flag was turned on"/>

        <expand macro="fileload" />

    </inputs>
    <outputs>
	    <data name="purityX_tsv" format="tsv" label="${tool.name} on ${on_string}: tsv"
              from_work_dir="purityX_output.tsv" />
        <data name="purityX_rdata" format="rdata" label="${tool.name} on ${on_string}: RData"
              from_work_dir="purityX_output.RData" />
    </outputs>
    <tests>
        <test>
            <conditional name="file_load_conditional">
                <param name="file_load_select" value="yes"/>
                <param name="input" >
                    <collection type="list">
                        <element name="LCMSMS_2.mzML" value="LCMSMS_2.mzML"/>
                        <element name="LCMSMS_1.mzML" value="LCMSMS_1.mzML"/>
                        <element name="LCMS_2.mzML" value="LCMS_2.mzML"/>
                        <element name="LCMS_1.mzML" value="LCMS_1.mzML"/>
                    </collection>
                </param>
            </conditional>
            <conditional name="xgroups">
                <param name="xgroups" value="choose"/>
                <param name="xgroups_value" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15"/>
            </conditional>
            <param name="iw_norm" value="QE5" />
            <param name="xset" value="xset_group_LCMS_1_LCMS_2_LCMSMS_1_LCMSMS_2.RData"/>
            <output name="purityX_tsv" value="purityX_output.tsv" />
            <output name="purityX_rdata" value="purityX_output.RData" ftype="rdata" compare="sim_size"/>
        </test>
    </tests>
    <help><![CDATA[

===================================================================
Calculate anticipated precursor ion purity from LC-MS XCMS dataset
===================================================================
-----------
Description
-----------

Tool to calculate the anticipated precursor ion purity of selected precursor based on a prior LC-MS dataset. Based on
XCMS determined features

--------------
Output example
--------------
Output consists of the mz and intensity of the XCMS features (id based on the XCMS group id) and various
metrics regarding the anticipated precursor ion purity.

============= ============= ============= ================ ================ ================ ================ ================ ================
grpid         meanPurity    medianPurity  sdPurity         stdePurity	    cvPurity         pknmPurity       i                mz
============= ============= ============= ================ ================ ================ ================ ================ ================
1              1.00          1.00          0.0000           0.0000           0.0000           1                5404920          100.0758
------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
2              0.59          0.57          0.3016           0.1508           50.570           3                8793845          101.0084
------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
3              0.08          0.07          0.0784           0.0164           29.643           4                1526502          100.9781
------------- ------------- ------------- ---------------- ---------------- ---------------- ---------------- ---------------- ----------------
4              1.00          1.00          0.0000           0.0000           0.0000           1                42513139         102.0914
============= ============= ============= ================ ================ ================ ================ ================ ================


(Note - the additional peakID column is the same as grpid. Included for compatibility with other Galaxy tools)


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