comparison align_samples.xml @ 2:7b6f148bd99f draft default tip

"planemo upload for repository https://github.com/computational-metabolomics/dimspy-galaxy commit 80069808371b58f45da0c8133c27d67ac1a5b448"

1:c72868b80c29

<tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy@GALAXY_TOOL_VERSION@">
    <description> - Align peaks across Peaklists</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

        --output '$hdf5_file_out'
        #if $filelist
            --filelist '$filelist'
        #end if
        --ppm $ppm
        #if $hdf5_to_txt.standard
            &&
            @HDF5_PM_TO_TXT@
        #end if
        #if $hdf5_to_txt.comprehensive

        <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklists (HDF5 file)" help="" />
        <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" optional="true" label="Filelist / Samplelist" help="Only provide a filelist if you like to exclude Peaklists, update the metadata (e.g. classLabel), or if you have not provided a filelist for  Process Scans or Replicate Filter." />
        <param name="ppm" argument="--ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." />
        <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
        <expand macro="hdf5_pm_to_txt" />
    </inputs>
    <outputs>
        <expand macro="outputs_peak_intensity_matrix" />
    </outputs>
    <tests>

                <param name="standard" value="True"/>
                <param name="comprehensive" value="False"/>
                <param name="samples_representations" value="rows"/>
                <param name="matrix_attr" value="intensity"/>
            </conditional>
            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
            <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
        </test>
        <test>
            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>

2:7b6f148bd99f

<tool id="dimspy_align_samples" name="Align Samples" version="@TOOL_VERSION@+galaxy1">
    <description> - Align peaks across Peaklists</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

        --output '$hdf5_file_out'
        #if $filelist
            --filelist '$filelist'
        #end if
        --ppm $ppm
        --ncpu \${GALAXY_SLOTS:-1}
        --block-size $adv.block_size
        #if $hdf5_to_txt.standard
            &&
            @HDF5_PM_TO_TXT@
        #end if
        #if $hdf5_to_txt.comprehensive

        <param name="hdf5_file_in" argument="--input" type="data" format="h5" label="Peaklists (HDF5 file)" help="" />
        <param name="filelist" argument="--filelist" type="data" format="tsv,tabular" optional="true" label="Filelist / Samplelist" help="Only provide a filelist if you like to exclude Peaklists, update the metadata (e.g. classLabel), or if you have not provided a filelist for  Process Scans or Replicate Filter." />
        <param name="ppm" argument="--ppm" type="float" value="2.0" label="Ppm error tolerance" help="Maximum tolerated m/z deviation across samples in parts per million (ppm)." />
        <param name="delimiter" argument="--delimiter" type="hidden" value="tab" />
        <expand macro="hdf5_pm_to_txt" />
        <section name="adv" title="Advanced options" expanded="False">
            <param name="block_size" argument="--block-size" type="integer" value="5000" label="Block size" help="The size of each block of peaks to perform clustering on." />
        </section>
    </inputs>
    <outputs>
        <expand macro="outputs_peak_intensity_matrix" />
    </outputs>
    <tests>

                <param name="standard" value="True"/>
                <param name="comprehensive" value="False"/>
                <param name="samples_representations" value="rows"/>
                <param name="matrix_attr" value="intensity"/>
            </conditional>
            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
            <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
        </test>
        <test>
            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>
            <param name="ppm" value="2.0"/>
            <param name="delimiter" value="tab"/>
            <conditional name="hdf5_to_txt" >
                <param name="standard" value="True"/>
                <param name="comprehensive" value="False"/>
                <param name="samples_representations" value="rows"/>
                <param name="matrix_attr" value="intensity"/>
            </conditional>
            <section name="adv">
                <param name="block_size" value="10000"/>
            </section>
            <output name="hdf5_file_out" file="pm_as.h5" ftype="h5" compare="sim_size"/>
            <output name="matrix_file_out" file="peak_matrix_as.txt" ftype="tsv"/>
        </test>
        <test>
            <param name="hdf5_file_in" value="pls_rf.h5" ftype="h5"/>