comparison flagRemove.xml @ 15:b71677d4f958 draft default tip

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit cb903cd93f9378cfb5eeb68512a54178dcea7bbc

14:568e12663295

<tool id="mspurity_flagremove" name="msPurity.flagRemove" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
    <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds
        (e.g. RSD of intensity and retention time).
    </description>

    <macros>
        <import>macros.xml</import>
    </macros>

    <expand macro="requirements" />

    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command interpreter="Rscript"><![CDATA[
        flagRemove.R
                --xset_path=$xset_path
                --out_dir=.

                #if $sample_flag.sample_flag=='update'
                    --rsd_i_sample=$sample_flag.rsd_i_sample
                    --minfrac_sample=$sample_flag.minfrac_sample
                    --ithres_sample=$sample_flag.ithres_sample
                #end if

                #if $blank_flag.blank_flag=='update'
                    --rsd_i_blank=$blank_flag.rsd_i_blank
                    --minfrac_blank=$blank_flag.minfrac_blank
                    --ithres_blank=$blank_flag.ithres_blank
                    --blank_class=$blank_flag.blank_class
                #end if

                #if $peak_removal.peak_removal=='remove'
                    --remove_spectra
                    --minfrac_xcms=$peak_removal.minfrac_xcms
                    --mzwid=$peak_removal.mzwid
                    --bw=$peak_removal.bw
                #end if

                #if $advanced.advanced=='update'
                    --egauss_thr=$advanced.egauss_thr
                    --polarity=$advanced.polarity
                    --grp_rm_ids=$advanced.grp_rm_ids
                    --xset_name=$advanced.xset_name
                    $advanced.temp_save.value

                #end if
                #if $choose_samp.choose_samp=='yes'
                        --samplelist=$choose_samp.samplelist
                #end if
    ]]></command>
    <inputs>
        <param type="data" name="xset_path" format='rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata'
                help="The path to the xcmsSet object saved as an RData file"/>
        <conditional name="sample_flag">
            <param name="sample_flag" type="select" label="Change biological sample flag parameters?">
                <option value="update" >Update biological sample flag parameters</option>
                <option value="" selected="true">Use default biological sample flag parameters</option>
            </param>
            <when value="">
            </when>
            <when value="update">
                <param name="rsd_i_sample" type="text" label="rsd_i_sample" value="NA"
                    help="Relative Standard Deviation threshold for the sample classes (--rsd_i_sample)"/>
                <param name="minfrac_sample" type="float" label="minfrac_sample" value="0.5" min="0.0" max="1"
                    help="minimum fraction of files for features needed for the sample classes (--minfrac_sample)"/>
                <param name="rsd_rt_sample" type="text" label="rsd_rt_sample" value="NA"
                    help="Relative standard Deviation threshold for the retention time of the sample
                     classes (--rsd_rt_sample)"/>
                <param name="ithres_sample" type="text" label="ithres_sample" value="NA"
                    help="Intensity threshold for the sample (--ithres_sample)"/>
            </when>
        </conditional>
        <conditional name="blank_flag">
            <param name="blank_flag" type="select" label="Change blank flag parameters?">
                <option value="update" >Update blank flag parameters</option>
                <option value="" selected="true">Use default blank flag parameters</option>
            </param>
            <when value="">
            </when>
            <when value="update">
                <param name="blank_class" type="text" label="blank_class" value="blank"
                help="A string representing the class that will be used for the blank (--blank_class)"/>
                <param name="rsd_i_blank" type="text" label="rsd_i_blank" value="NA"
                    help="RSD threshold for the blank (--rsd_i_blank)"/>
                <param name="minfrac_blank" type="float" label="minfrac_blank" value="0.5" min="0.0" max="1"
                    help="minimum fraction of files for features needed for the blank (--minfrac_blank)"/>
                <param name="rsd_rt_blank" type="text" label="rsd_rt_blank" value="NA"
                    help="RSD threshold for the retention time of the blank (--rsd_rt_blank)"/>
                <param name="ithres_blank" type="text" label="ithres_blank" value="NA"
                    help="Intensity threshold for the blank (--ithres_blank)"/>
                <param name="s2b" type="float" label="s2b" value="10"
                    help="fold change (sample/blank) needed for sample peak to be allowed. e.g.
                    if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
                    1000/10 = 100, so sample has fold change higher than the threshold and the peak
                    is not considered a blank (--s2b)"/>
            </when>
        </conditional>
        <conditional name="peak_removal">
            <param name="peak_removal" type="select" label="Remove peaks from xcmsSet object?">
                <option value="remove" >Remove peaks and re-group</option>
                <option value="" selected="true">Only flag peaks (do not remove and re-group)</option>
            </param>
            <when value="">
            </when>
            <when value="remove">
                 <param name="minfrac_xcms" type="float" label="minfrac_xcms" value="0.7" min="0.0" max="1"
                    help="minfrac for xcms  grouping (--minfrac_xcms)"/>
                 <param name="mzwid" type="float" label="mzwid" value="0.001"
                    help="mzwid for xcms  grouping (--minfrac_xcms)"/>
                <param name="bw" type="float" label="bw" value="5"
                    help="bw for xcms  grouping(--minfrac_xcms)"/>
            </when>
        </conditional>
        <conditional name="advanced">
            <param name="advanced" type="select" label="Advanced parameters">
                <option value="update" >Update advanced and testing parameters</option>
                <option value="" selected="true">Use default advanced parameters</option>
            </param>
            <when value="">
            </when>
            <when value="update">
                <param name="egauss_thr" type="text" label="egauss_thr" value="NA"
                    help="Threshold for filtering out non gaussian shaped peaks. Note this only works
                          if the 'verbose columns' and 'fit gauss' was used with xcms (--egauss_thr)"/>
                <param name="temp_save" type="boolean" label="temp_save" checked="false" truevalue="--temp_save" falsevalue=""
                    help="Assign True if files for each step saved (for testing purposes) (--temp_save)"/>
                <param name="polarity" type="select" label="polarity"
                    help="polarity (just used for naming purpose when files are saved) (--polarity)">
                    <option value="positive">Positive</option>
                    <option value="negative" >Negative</option>
                    <option value="NA" selected="true">NA</option>
                </param>
                <param name="grp_rm_ids" type="text" label="grp_rm_ids" value="NA"
                help="comma seperated list of grouped_xcms peak ids to remove (corresponds to the row from xcms::group output)
                      e.g '1,20,30,56'
                 (--grp_rm_ids)"/>
                <param name="xset_name" type="text" label="xset_name" value="xset"
                    help="Name of the xcmsSet object within the RData file (--xset_name)"/>
            </when>
        </conditional>
        <conditional name="choose_samp">
            <param name="choose_samp" type="select" label="Samplelist">
                        <option value="yes" >Use samplelist</option>
                        <option value="" selected="true">Don't use samplelist</option>
            </param>
            <when value="">
            </when>
            <when value="yes">
                <param name="samplelist" type="data" label="samplelist" format="tsv,tabular"
                       help="A samplelist can be provided to find an appriopiate blank class (requires a column 'blank' where 'yes' indicates the class should be used as the blank (--samplelist)"/>

            </when>
        </conditional>
    </inputs>
    <outputs>

15:b71677d4f958

<tool id="mspurity_flagremove" name="msPurity.flagRemove" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
    <description>Tool to flag and remove XCMS grouped peaks from the xcmsSet object based on various thresholds
        (e.g. RSD of intensity and retention time).
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        Rscript '$__tool_directory__/flagRemove.R'
                --xset_path='$xset_path'
                --out_dir=.

                #if $sample_flag.sample_flag=='update'
                    --rsd_i_sample='$sample_flag.rsd_i_sample'
                    --minfrac_sample='$sample_flag.minfrac_sample'
                    --ithres_sample='$sample_flag.ithres_sample'
                #end if

                #if $blank_flag.blank_flag=='update'
                    --rsd_i_blank='$blank_flag.rsd_i_blank'
                    --minfrac_blank='$blank_flag.minfrac_blank'
                    --ithres_blank='$blank_flag.ithres_blank'
                    --blank_class='$blank_flag.blank_class'
                #end if

                #if $peak_removal.peak_removal=='remove'
                    --remove_spectra
                    --minfrac_xcms='$peak_removal.minfrac_xcms'
                    --mzwid='$peak_removal.mzwid'
                    --bw='$peak_removal.bw'
                #end if

                #if $advanced.advanced=='update'
                    --egauss_thr='$advanced.egauss_thr'
                    --polarity='$advanced.polarity'
                    --grp_rm_ids='$advanced.grp_rm_ids'
                    --xset_name='$advanced.xset_name'
                    '$advanced.temp_save.value'

                #end if
                #if $choose_samp.choose_samp=='yes'
                        --samplelist='$choose_samp.samplelist'
                #end if
    ]]></command>
    <inputs>
        <param argument="--xset_path" type="data" format='rdata.xcms.raw,rdata.xcms.group,rdata.xcms.retcor,rdata.xcms.fillpeaks,rdata'
                help="The path to the xcmsSet object saved as an RData file"/>
        <conditional name="sample_flag">
            <param argument="sample_flag" type="select" label="Change biological sample flag parameters?">
                <option value="update" >Update biological sample flag parameters</option>
                <option value="" selected="true">Use default biological sample flag parameters</option>
            </param>
            <when value="">
            </when>
            <when value="update">
                <param argument="--rsd_i_sample" type="text" label="rsd_i_sample" value="NA"
                    help="Relative Standard Deviation threshold for the sample classes"/>
                <param argument="--minfrac_sample" type="float" label="minfrac_sample" value="0.5" min="0.0" max="1"
                    help="minimum fraction of files for features needed for the sample classes"/>
                <param argument="--rsd_rt_sample" type="text" label="rsd_rt_sample" value="NA"
                    help="Relative standard Deviation threshold for the retention time of the sample
                     classes"/>
                <param argument="--ithres_sample" type="text" label="ithres_sample" value="NA"
                    help="Intensity threshold for the sample"/>
            </when>
        </conditional>
        <conditional name="blank_flag">
            <param argument="blank_flag" type="select" label="Change blank flag parameters?">
                <option value="update" >Update blank flag parameters</option>
                <option value="" selected="true">Use default blank flag parameters</option>
            </param>
            <when value="">
            </when>
            <when value="update">
                <param argument="--blank_class" type="text" label="blank_class" value="blank"
                help="A string representing the class that will be used for the blank"/>
                <param argument="--rsd_i_blank" type="text" label="rsd_i_blank" value="NA"
                    help="RSD threshold for the blank"/>
                <param argument="--minfrac_blank" type="float" label="minfrac_blank" value="0.5" min="0.0" max="1"
                    help="minimum fraction of files for features needed for the blank"/>
                <param argument="--rsd_rt_blank" type="text" label="rsd_rt_blank" value="NA"
                    help="RSD threshold for the retention time of the blank"/>
                <param argument="--ithres_blank" type="text" label="ithres_blank" value="NA"
                    help="Intensity threshold for the blank"/>
                <param argument="--s2b" type="float" label="s2b" value="10"
                    help="fold change (sample/blank) needed for sample peak to be allowed. e.g.
                    if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
                    1000/10 = 100, so sample has fold change higher than the threshold and the peak
                    is not considered a blank"/>
            </when>
        </conditional>
        <conditional name="peak_removal">
            <param name="peak_removal" type="select" label="Remove peaks from xcmsSet object?">
                <option value="remove" >Remove peaks and re-group</option>
                <option value="" selected="true">Only flag peaks (do not remove and re-group)</option>
            </param>
            <when value="">
            </when>
            <when value="remove">
                 <param argument="--minfrac_xcms" type="float" label="minfrac_xcms" value="0.7" min="0.0" max="1"
                    help="minfrac for xcms  grouping"/>
                 <param argument="--mzwid" type="float" label="mzwid" value="0.001"
                    help="mzwid for xcms  grouping"/>
                <param argument="--bw" type="float" label="bw" value="5"
                    help="bw for xcms  grouping"/>
            </when>
        </conditional>
        <conditional name="advanced">
            <param name="advanced" type="select" label="Advanced parameters">
                <option value="update" >Update advanced and testing parameters</option>
                <option value="" selected="true">Use default advanced parameters</option>
            </param>
            <when value="">
            </when>
            <when value="update">
                <param argument="--egauss_thr" type="text" label="egauss_thr" value="NA"
                    help="Threshold for filtering out non gaussian shaped peaks. Note this only works
                          if the 'verbose columns' and 'fit gauss' was used with xcms"/>
                <param argument="--temp_save" type="boolean" label="temp_save" checked="false" truevalue="--temp_save" falsevalue=""
                    help="Assign True if files for each step saved (for testing purposes)"/>
                <param argument="--polarity" type="select" label="polarity"
                    help="polarity (just used for naming purpose when files are saved)">
                    <option value="positive">Positive</option>
                    <option value="negative" >Negative</option>
                    <option value="NA" selected="true">NA</option>
                </param>
                <param argument="--grp_rm_ids" type="text" label="grp_rm_ids" value="NA"
                help="comma seperated list of grouped_xcms peak ids to remove (corresponds to the row from xcms::group output)
                      e.g '1,20,30,56'"/>
                <param argument="--xset_name" type="text" label="xset_name" value="xset"
                    help="Name of the xcmsSet object within the RData file"/>
            </when>
        </conditional>
        <conditional name="choose_samp">
            <param name="choose_samp" type="select" label="Samplelist">
                        <option value="yes" >Use samplelist</option>
                        <option value="" selected="true">Don't use samplelist</option>
            </param>
            <when value="">
            </when>
            <when value="yes">
                <param argument="--samplelist" type="data" label="samplelist" format="tsv,tabular"
                       help="A samplelist can be provided to find
                       an appriopiate blank class (requires a column 'blank' where 'yes' indicates the
                       class should be used as the blank) "/>

            </when>
        </conditional>
    </inputs>
    <outputs>