view cameradims.xml @ 20:8e33abdebc57 draft default tip

planemo upload for repository https://github.com/computational-metabolomics/dma-tools-galaxy commit 14435cfc042911bf1ee409f5a0d5ef908f5feec0-dirty

<tool id="cameradims" name="CAMERA_DIMS" version="0.2.6">
    <description>Modification of the R package CAMERA to work on DIMS data</description>
    <requirements>
        <requirement type="package" version="0.2.9">r-cameradims</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript"><![CDATA[
        cameradims.R --in_file $peaks_file
                      --out_dir .
                      --ppm_adduct $ppm_adduct
                      --ppm_iso $ppm_iso
                      --mzabs_adduct $mzabs_adduct
                      --mzabs_iso $mzabs_iso
                      --maxiso $maxiso
                      --maxcharge $maxcharge
                      --maxmol $maxmol
                      --polarity $polarity
                      --rule_type $ruleset.ruleset
                      #if $ruleset.ruleset == 'user'
                        --rule_path $ruleset.rulesfile
                      #end if
                      #if $export_ruleset
                        --export_ruleset
                      #end if
                        --intensity_filter=$intensity_filter
    ]]></command>

    <inputs>
        <param type="data" name="peaks_file" format="tabular,tsv"
                help="tsv or tabular file with mz and intensity columns"/>
        <param name="ppm_adduct" type="float" label="ppm (adduct)" value="5"
                    help="general ppm error (adduct)"/>
        <param name="ppm_iso" type="float" label="ppm (iso)" value="5"
                    help="general ppm error (iso)"/>
        <param name="mzabs_adduct" type="float" label="mzabs (adduct)" value="0.015"
                    help="general absolute error in m/z"/>
        <param name="mzabs_iso" type="float" label="mzabs (iso)" value="0.015"
                    help="general absolute error in m/z"/>
        <param name="maxmol" type="integer" label="maxmol" value="3"
                    help="highest number(n) of allowed clusterion [nM+ion] (argument called multiplier in findAdducts())"/>
        <param name="maxiso" type="integer" label="maxiso" value="4"
                    help="max number of expected isotopes"/>
        <param name="maxcharge" type="integer" label="maxcharge" value="3"
                    help="max ion charge for finding isotopes"/>
        <param name="polarity" type="select" label="polarity" help="Which polarity mode was used for measuring of the ms sample" >
            <option value="pos" selected="true">positive</option>
            <option value="neg">negative</option>
        </param>

        <param name="intensity_filter" type="float" label="Intensity filter" value="5000"
                    help="Filter out any peaks that have intensity less than this value. (Adduct calculation may take
                          a very long time if peaks are not filtered before hand)  "/>

        <conditional name="ruleset">
            <param name="ruleset" type="select" label="Rules for adducts" >
                <option value="primary adducts" >Primary adducts ([M+Na]+, [M+K]+ and [M+NH4]+")</option>
                <option value="extended" selected="true" >Extended adducts</option>
                <option value="extended_large" >Extended adducts (large)</option>
                <option value="user" >Provide a csv file of the rules to use</option>
            </param>
            <when value="user">
                        <param type="data" name="rulesfile" format="tsv, tabular"
                help="User supplied rules file used to to calculate adducts, should contain the following
                      columns name,nmol,charge,massdiff,oidscore,quasi,ips.
                      If using the adducts to guide fragmentation then the frag_score column should be included. Where
                      a score of 1 indicates the adduct is the best adduct form to fragment"/>
            </when>
            <when value="extended">
            </when>
            <when value="primary adducts">
            </when>
        </conditional>
        <param name="export_ruleset" type="boolean" label="Export the adduct ruleset used?" help=""/>
    </inputs>
    <outputs>
	    <data name="camera_annotated_map" format="tsv" label="${tool.name} on ${on_string}: map"
              from_work_dir="camera_annotated_map.txt"  />
        <data name="camera_annotated_peaklist" label="${tool.name} on ${on_string}: peaklist"
              from_work_dir="camera_annotated_peaklist.txt" format="tsv"/>
        <data name="ruleset" label="${tool.name} on ${on_string}: ruleset"
              from_work_dir="ruleset.txt"  format="tsv">
            <filter>export_ruleset is True</filter>
        </data>



    </outputs>
    <tests>
        <test>
            <param name="peaks_file" value="peaklist_in.tsv" ftype="tsv"/>
            <output name="camera_annotated_peaklist" value="camera_annotated_peaklist.txt"/>
            <output name="camera_annotated_map" value="camera_annotated_map.txt"/>
        </test>
    </tests>
    <help><![CDATA[
    cameraDIMS

    ]]></help>
    <citations>
            <citation type="doi">10.1021/ac202450g</citation>
    </citations>
</tool>