comparison filtering.xml @ 4:58376f5a6319 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d

3:4b5513e25902

<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.2">
    <description>tool for filtering mass spectrometry imaging data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

        ## Range y coordinates
        minimumy = min(coord(msidata)[,2])
        maximumy = max(coord(msidata)[,2])
        ## Store features for QC plot
        featuresinfile = mz(msidata)

## Next steps will only run if there are more than 0 pixels/features in the file

if (ncol(msidata)>0 & nrow(msidata) >0)
{

    #end if

    ############################# QC data #####################################

    ## dataframe for QC of pixel distribution
    position_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata)))
    colnames(position_df)[3] = "annotation"
    position_df\$annotation = factor(position_df\$annotation)
    gc()

}else{
    print("Inputfile has no intensities > 0")

                </param>
            </when>
        </conditional>
        <param name="imzml_output" type="select" display = "radio" optional = "False"
               label="Output format" help= "Choose the output format">
                <option value="imzml_format" selected="True">imzML</option>
                <option value="rdata_format">RData</option>
        </param>
    </inputs>

    <outputs>
        <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">

**Output**

- MSI data as imzML file or .RData (can be read with the Cardinal package in R)
- pdf with heatmap showing the pixels that are left after filtering and histograms of kept and removed m/z


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

4:58376f5a6319

<tool id="cardinal_filtering" name="MSI filtering" version="@VERSION@.3">
    <description>tool for filtering mass spectrometry imaging data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">

        ## Range y coordinates
        minimumy = min(coord(msidata)[,2])
        maximumy = max(coord(msidata)[,2])
        ## Store features for QC plot
        featuresinfile = mz(msidata)

        all_df = cbind(coord(msidata)[,1:2], rep("removed pixels", times=ncol(msidata)))
        colnames(all_df)[3] = "annotation"

## Next steps will only run if there are more than 0 pixels/features in the file

if (ncol(msidata)>0 & nrow(msidata) >0)
{

    #end if

    ############################# QC data #####################################

    ## dataframe for QC of pixel distribution

    remaining_df = cbind(coord(msidata)[,1:2], rep("remaining pixels", times=ncol(msidata)))
    colnames(remaining_df)[3] = "annotation"
    position_df = rbind(all_df, remaining_df) 
    position_df[row.names(unique(position_df[,c("x", "y")])),]
    position_df\$annotation = factor(position_df\$annotation)
    gc()

}else{
    print("Inputfile has no intensities > 0")

                </param>
            </when>
        </conditional>
        <param name="imzml_output" type="select" display = "radio" optional = "False"
               label="Output format" help= "Choose the output format">
                <option value="imzml_format" >imzML</option>
                <option value="rdata_format" selected="True" >RData</option>
        </param>
    </inputs>

    <outputs>
        <data format="imzml" name="outfile_imzml" label="${tool.name} on ${on_string}: imzML">

**Output**

- MSI data as imzML file or .RData (can be read with the Cardinal package in R)
- pdf with heatmap showing the pixels that are removed and kept as well as histograms of kept and removed m/z


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