comparison build_matrix.xml @ 1:31a21ba2c5ea draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit bb79cb8cad3bc1433bff7caf9d7b45e7993dd470

0:1bf008d6d54e

      ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
@CMD_imports@
peaks = esc.ct.load_peaks('$peaks_file')
esc.ct.norm_peaks(peaks, extension=$extension)
esc.ct.bld_mtx_bed(
    fragment_file='fragments.gz',
    feature_region=peaks,
    #if $reference_chr.chr_select == 'custom'
        #set $chromosomes = ([x.strip() for x in str($reference_chr.chromosomes).split(',')])

]]></configfile>
    </configfiles>
    <inputs>
        <param name="fragment_file" type="data" format="bed" label="ATAC fragments file" />
        <param name="peaks_file" type="data" format="tabular" label="Features file" help="Peaks BED file or MACS2 narrowPeak file"/>
        <param name="extension" type="integer" value="0" min="0" label="Number of bases to extend both sides of peaks" />
        <conditional name="reference_chr">
            <param name="chr_select" type="select" label="Select the chromosomes of the species you are considering" >
                <option value="human">Human chromosomes ['1', '2', '3', ... , '22', 'X', 'Y']</option>
                <option value="mouse">Mouse chromosomes ['1', '2', '3', ... ', '19', 'X', 'Y']</option>
                <option value="custom">Custom list of chromosomes</option>

            <filter>advanced_common['show_log']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <!-- count matrix -->
            <param name="fragment_file" value="chrY.fragments.bed" />
            <param name="peaks_file" value="chrY.peaks.bed" />
            <conditional name="reference_chr">
                <param name="chr_select" value="custom" />
                <param name="chromosomes" value="Y" />
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="anndata_out" file="chrY.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
    </tests>
  <help>
.. class:: infomark

1:31a21ba2c5ea

      ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
@CMD_imports@
peaks = esc.ct.load_peaks('$peaks_file')
#if $peak_size.normalize == 'yes' 
esc.ct.norm_peaks(peaks, extension=$peak_size.extension)
#end if
esc.ct.bld_mtx_bed(
    fragment_file='fragments.gz',
    feature_region=peaks,
    #if $reference_chr.chr_select == 'custom'
        #set $chromosomes = ([x.strip() for x in str($reference_chr.chromosomes).split(',')])

]]></configfile>
    </configfiles>
    <inputs>
        <param name="fragment_file" type="data" format="bed" label="ATAC fragments file" />
        <param name="peaks_file" type="data" format="tabular" label="Features file" help="Peaks BED file or MACS2 narrowPeak file"/>
        <conditional name="peak_size">
            <param name="normalize" type="select" label="Normalize peak sizes?" >
                <option value="no" selected="true">No, keep the peaks as they are</option>
                <option value="yes">Yes, normalize the peaks to equal length from the center</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="extension" type="integer" value="0" min="0" label="Number of bases to extend both sides from the center of the peak" help="All resulting peaks will have the same length"/>
            </when>
        </conditional>
        <conditional name="reference_chr">
            <param name="chr_select" type="select" label="Select the chromosomes of the species you are considering" >
                <option value="human">Human chromosomes ['1', '2', '3', ... , '22', 'X', 'Y']</option>
                <option value="mouse">Mouse chromosomes ['1', '2', '3', ... ', '19', 'X', 'Y']</option>
                <option value="custom">Custom list of chromosomes</option>

            <filter>advanced_common['show_log']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <!-- default params -->
            <param name="fragment_file" value="chrY.fragments.bed" />
            <param name="peaks_file" value="chrY.peaks.bed" />
            <conditional name="reference_chr">
                <param name="chr_select" value="custom" />
                <param name="chromosomes" value="Y" />
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="anndata_out" file="chrY.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
        <test expect_num_outputs="2">
            <!-- normalized peaks -->
            <param name="fragment_file" value="chrY.fragments.bed" />
            <param name="peaks_file" value="chrY.peaks.bed" />
            <conditional name="peak_size">
                <param name="normalize" value="yes" />
                <param name="extension" value="250" />
            </conditional>
            <conditional name="reference_chr">
                <param name="chr_select" value="custom" />
                <param name="chromosomes" value="Y" />
            </conditional>
            <section name="advanced_common">
                <param name="show_log" value="true" />
            </section>
            <output name="anndata_out" file="chrY_norm_peaks.h5ad" ftype="h5ad" compare="sim_size"/>
        </test>
    </tests>
  <help>
.. class:: infomark