comparison process_scans.xml @ 1:deafa30d6570 draft

"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 680116d0cf6a6d7246cba655452dea43269aeba4"

0:62c4813fbe7a

    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
        #if $data.input[0].is_of_type("zip")
            dimspy process-scans
            --input $data.input[0]
        #else
            #for $fn in $data.input
                ln -s '$fn' '$fn.name'
                &&
            #end for

----------------

Description
-----------

Standard DIMS processing workflow: **Process Scans** -> Replicate Filter -> Align Samples -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> Matrix processing -> Statistics

This tool is used to generate a single mass spectral peaklist for each of the data files defined in the ‘Filelist/Samplelist’. The tool extracts mass spectral peaks from a data file (in either .mzML or .RAW format) and then filters these in accordance with user-defined parameter settings. All peaks remaining after filtering are hierarchically clustered in one-dimension, during which pairs of peaks with similar m/z values are grouped together if the difference between their m/z values, when divided by the average of their m/z values and multiplied by 1 x 10\ :sup:`6` \, equates to less-than the user-defined ppm error tolerance.

**IMPORTANT:** when using .mzML files generated using the Proteowizard tool, SIM-type scans will only be treated as spectra if the ‘simAsSpectra’ filter was set to true during the conversion process, e.g.:

1:deafa30d6570

    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
    <![CDATA[
        #if $data.input[0].is_of_type("zip")
            dimspy unzip 
            --input $data.input[0]
            --output ./data
            &&
            dimspy process-scans
            --input ./data
        #else
            #for $fn in $data.input
                ln -s '$fn' '$fn.name'
                &&
            #end for

----------------

Description
-----------

Standard DIMS processing workflow: **Process Scans** -> [Replicate Filter] -> Align Samples -> [Missing values sample filter] -> Blank Filter -> Sample Filter -> [Missing values sample filter] -> Pre-processing -> Statistics

This tool is used to generate a single mass spectral peaklist for each of the data files defined in the ‘Filelist/Samplelist’. The tool extracts mass spectral peaks from a data file (in either .mzML or .RAW format) and then filters these in accordance with user-defined parameter settings. All peaks remaining after filtering are hierarchically clustered in one-dimension, during which pairs of peaks with similar m/z values are grouped together if the difference between their m/z values, when divided by the average of their m/z values and multiplied by 1 x 10\ :sup:`6` \, equates to less-than the user-defined ppm error tolerance.

**IMPORTANT:** when using .mzML files generated using the Proteowizard tool, SIM-type scans will only be treated as spectra if the ‘simAsSpectra’ filter was set to true during the conversion process, e.g.: