view lcms-interval-scheduling.xml @ 2:ac50ece6573e draft

planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit d4159f1962ef3fe37dd4f3047e4050afe013c15a-dirty

<tool id="lcms_interval_scheduling" name="lcms_interval_scheduling" version="0.0.2">
    <requirements>
        <requirement type="package" >r</requirement>
	    <requirement type="package" >r-optparse</requirement>
        <requirement type="package" >r-xcmswrapper</requirement>
    </requirements>
    <description>Generate target lists from LC-MS features for a fragmentation experiment
    </description>

    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript"><![CDATA[
        lcms-interval-scheduling.R

                --sample_peaklist=$sample_peaklist
                --blank_peaklist=$blank_peaklist
                --topn=$topn
                --out_dir=.
                --method=$method_select.method
                #if $method_select.method=='metshot'
                    #if $method_select.fillgaps
                        --fillgaps
                    #end if
                #elif $method_select.method=='simple'
                    --maxms2=$method_select.maxms2
                    --ilimit=$method_select.ilimit
                #else
                    --overlappingP=$method_select.overlappingP
                #end if
                --widthFactor=$widthFactor
                --minWidth=$minWidth
                --shift=$shift
                --samplelistNm=$samplelistNm
                #if $fullpw
                   --fullpw
                #end if
                --b_widthFactor=$b_widthFactor
                --b_shift=$b_shift
                --b_exclu_limit=$b_exclu_limit
                --b_minWidth=$b_minWidth
                --polarity=$polarity
                #if $dma_nearline_cond.dma=='yes'
                    --blankClass=$dma_nearline_cond.blankClass
                    --filterS=$dma_nearline_cond.filterS
                    --dmaNearline
                #end if
                --intensityCN=$intensityCN
                --sortCN=$sortCN
    ]]></command>
    <inputs>
        <param type="data" name="sample_peaklist" label="Sample peaklist" format="tsv,tabular"
                help="The peaklist from the samples to be scheduled for fragmentation"/>

        <param type="data" name="blank_peaklist" label="Blank peaklist" format="tsv,tabular"
                help="The peaklist of blank features to avoid when performing fragmentation"/>

        <param type="data" name="topn" label="Topn blank peaklist" format="tsv,tabular"
                help="The top (n) blank peaks determined from windows of the spectrum (i.e. not using XCMS)"/>

        <conditional name="method_select">
            <param name="method" type="select" label="Nearline method">
                <option value="simple" >Simple nearline (divide equally amongst runs) </option>
                <option value="interval">Interval schedule with defined overlap</option>
                <option value="interval_min_overlap" selected="true">Interval schedule with defined overlap. Overlap is also minimized</option>
                <option value="metshot">Original metshot algorithm (No overlapping features)</option>
            </param>
            <when value="metshot">
                <param name="fillGaps" type="boolean" label="Fill gaps"/>
            </when>
            <when value="simple">
                <param name="maxms2" type="integer" label="Max MS2 per run" value="2000"/>
                <param name="ilimit" type="float" label="Intensity (peak area) limit to be included" value="5000"/>
            </when>
            <when value="interval">
                <param name="overlappingP" type="integer" label="Max number of overlapping peaks" value="10"/>
            </when>
            <when value="interval_min_overlap">
                <param name="overlappingP" type="integer" label="Max number of overlapping peaks" value="10"/>
            </when>
        </conditional>

        <param name="widthFactor" type="float" label="Width factor" value="1"
                    help="Increase the width of the peaks by the chosen factor "/>

        <param name="minWidth" type="float" label="Minimum width of peak (sec)" value="5"
                    help="The time range will always be >= to this value (even if the prior peak width is calculated
                          to be smaller)"/>

        <param name="shift" type="float" label="Shift (sec)" value="0" help="Shift all the peaks by value to account for drift"/>
        <param name="samplelistNm" type="integer" label="Number of MS2 runs to perform" value="4"/>
        <param name="fullpw" type="boolean" label="Use full peak width?" help="" />
        <param name="b_widthFactor" type="float" label="Width factor (for blank)" value="2"
                    help="Increase the width of the peaks by the chosen factor "/>

        <param name="b_minWidth" type="float" label="Minimum width of peak (sec) (for blank)" value="5"
                    help="The time range will always be >= to this value (even if the prior peak width is calculated
                          to be smaller) (for blank)"/>


        <param name="b_shift" type="float" label="Shift (for blank) (sec)" value="0" help="Shift all the peaks by value to account for drift"/>
        <param name="b_exclu_limit" type="integer" label="Exclusion limit" value="5000" help="Limit of peaks to put on exclusion limit"/>
        <param name="polarity" type="select" label="Polarity">
                <option value="positive" selected="true" >Positive</option>
                <option value="negative" >Negative</option>
        </param>

        <param name="sortCN" type="text" label="column of sample peaklist to order by" value="totalS"
                       help="default value corresponds if the tool 'deconrank' has been run prior. The 'total score'
                           column is based on multiple criteria (see deconrank tool).
                            If not using the deconrank tool, any other column can be used e.g. intensity (peak area)"/>

        <param name="intensityCN" type="text" label="column to use for intensity (peak area) for sample" value="i"/>


        <conditional name="dma_nearline_cond">
            <param name="dma" type="select" label="Use as part of DMA nearline workflow?"
                   help="If using within the nearline LC-MS workflow then certain processing needs to be performed,
                         including filtering out peaks that are not to be scheduled">
                <option value="yes">Yes</option>
                <option value="no" select="no">No</option>
            </param>
            <when value="yes">
                <param name="blankClass" type="text" label="Blank class" value="blank"
                       help="Note that this will have to change if the blank class has a different name. Uses the valid
                             column e.g. [blank_name]_valid.
                             If he value is 1 (we keep) if 0 (we do not use)" />
                <param name="filterS" type="text" label="Column name to filter sample on" value="excludedFinal"
                        help="This is a bit confusing.. But if this value is 1 then (we exclude) and if 0 (we keep for the
                               sample)"/>
            </when>
        </conditional>

    </inputs>
    <outputs>
        <collection name="inclusion_lists" type="list" label="${tool.name} on ${on_string}: inclusion lists">
            <discover_datasets pattern="(?P&lt;designation&gt;.+inclusion.+).csv" format="csv" directory="." />
        </collection>
        <collection name="exclusion_lists" type="list" label="${tool.name} on ${on_string}: exclusion lists">
            <discover_datasets pattern="(?P&lt;designation&gt;.+exclusion.+).csv" format="csv" directory="." />
        </collection>
        <data format="pdf" name="overlap_plots_positive"  label="${tool.name} on ${on_string}: overlap plots"
         from_work_dir="overlap_plots_positive.pdf"/>

    </outputs>
    <tests>
    </tests>
    <help><![CDATA[

    ]]></help>
</tool>