comparison signature.xml @ 14:5150d641d515 draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_signatures commit a54b915a3a245a71ca01ec9de2b5426cfb88504c

13:124f404b0fe7

<tool id="signature" name="Small RNA Signatures" version="3.4.2>">
    <description />
    <requirements>
        <requirement type="package" version="1.23.4">numpy</requirement>
        <requirement type="package" version="0.18.0">pysam</requirement>
        <requirement type="package" version="1.7.3">r-optparse</requirement>

           --output_h '$h_dataframe'
           --output_z '$z_dataframe' &&
        Rscript '$__tool_directory__'/signature.r
           --h_dataframe '$h_dataframe'
           --z_dataframe '$z_dataframe'
           --plot_method '$plot_method'
           --pdf '$pdf'
           --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs"
    ]]></command>
    <inputs>
        <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
        <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
        <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
        <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
        <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
        <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" />
        <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" />
        <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="plot_method" type="select">
            <option selected="True" value="global">Global</option>
            <option value="lattice">Lattice</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" label="z-signature data frame" name="z_dataframe">
            <actions>
                <action name="column_names" type="metadata" default="Chromosome,Overlap,Number_of_pairs,z-score" />

            <param name="maxquery" value="29" />
            <param name="mintarget" value="23" />
            <param name="maxtarget" value="29" />
            <param name="minscope" value="5" />
            <param name="maxscope" value="15" />
            <param name="plot_method" value="global" />
            <output file="h.tab" ftype="tabular" name="h_dataframe" />
            <output file="z.tab" ftype="tabular" name="z_dataframe" />
            <output file="global.pdf" ftype="pdf" name="pdf" />
        </test>
        <test>
            <param ftype="bam" name="input" value="sr_bowtie.bam" />
            <param name="minquery" value="23" />
            <param name="maxquery" value="29" />
            <param name="mintarget" value="23" />
            <param name="maxtarget" value="29" />
            <param name="minscope" value="5" />
            <param name="maxscope" value="15" />
            <param name="plot_method" value="lattice" />
            <output file="h.tab" ftype="tabular" name="h_dataframe" />
            <output file="z.tab" ftype="tabular" name="z_dataframe" />
            <output file="lattice.pdf" ftype="pdf" name="pdf" />
        </test>
    </tests>

14:5150d641d515

<tool id="signature" name="Small RNA Signatures" version="3.5.0">
    <description />
    <requirements>
        <requirement type="package" version="1.23.4">numpy</requirement>
        <requirement type="package" version="0.18.0">pysam</requirement>
        <requirement type="package" version="1.7.3">r-optparse</requirement>

           --output_h '$h_dataframe'
           --output_z '$z_dataframe' &&
        Rscript '$__tool_directory__'/signature.r
           --h_dataframe '$h_dataframe'
           --z_dataframe '$z_dataframe'
           --plot_method '$plot_options.plot_method'
           --pdf '$pdf'
           --title "Overlap Signatures of ${minquery}-${maxquery} against ${mintarget}-${maxtarget}nt small RNAs"
           #if $plot_options.plot_method == "global":
               --npairs_ylim $plot_options.npairs_ylim
               --npairszscore_ylim $plot_options.npairszscore_ylim
               --overlapprob_ylim $plot_options.overlapprob_ylim
               --overlapprobzscore_ylim $plot_options.overlapprobzscore_ylim
            #end if
    ]]></command>
    <inputs>
        <param format="bam" label="Compute signature from this bowtie standard output" name="input" type="data" />
        <param help="'23' = 23 nucleotides" label="Min size of query small RNAs" name="minquery" size="3" type="integer" value="23" />
        <param help="'29' = 29 nucleotides" label="Max size of query small RNAs" name="maxquery" size="3" type="integer" value="29" />
        <param help="'23' = 23 nucleotides" label="Min size of target small RNAs" name="mintarget" size="3" type="integer" value="23" />
        <param help="'29' = 29 nucleotides" label="Max size of target small RNAs" name="maxtarget" size="3" type="integer" value="29" />
        <param help="'1' = 1 nucleotide overlap" label="Minimal relative overlap analyzed" name="minscope" size="3" type="integer" value="1" />
        <param help="'1' = 1 nucleotide overlap" label="Maximal relative overlap analyzed" name="maxscope" size="3" type="integer" value="26" />
        <conditional name="plot_options">
            <param help="Signature can be computed globally or by item present in the alignment file" label="Graph type" name="plot_method" type="select">
                <option selected="True" value="global">Global</option>
                <option value="lattice">Lattice</option>
            </param>
            <when value="lattice" />
            <when value="global">
                <param name="npairs_ylim" type="integer" value="0" optional="true"
                       label="Maximum of Y-scale of the Numbers-of-pairs plot"
                       help="Interger. Leave 0 for self-determination of Y-scale" />
                <param name="npairszscore_ylim" type="integer" value="0" optional="true"
                       label="Maximum of Y-scale of the Number-of-pairs-Z−scores plot"
                       help="Integer. Leave 0 for self-determination of Y-scale" />
                <param name="overlapprob_ylim" type="integer" value="0" optional="true"
                       label="Maximum of Y-scale of the Overlap-probabilities plot"
                       help="Percent value as an Integer. Leave 0 for self-determination of % Y-scale" />
                <param name="overlapprobzscore_ylim" type="integer" value="0" optional="true"
                       label="Maximum of Y-scale of the Overlap-probabilities-Z−scores plot"
                       help="Interger. Leave 0 for self-determination of Y-scale" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" label="z-signature data frame" name="z_dataframe">
            <actions>
                <action name="column_names" type="metadata" default="Chromosome,Overlap,Number_of_pairs,z-score" />

            <param name="maxquery" value="29" />
            <param name="mintarget" value="23" />
            <param name="maxtarget" value="29" />
            <param name="minscope" value="5" />
            <param name="maxscope" value="15" />
            <conditional name="plot_options">
                <param name="plot_method" value="global" />
            </conditional>
            <output file="h.tab" ftype="tabular" name="h_dataframe" />
            <output file="z.tab" ftype="tabular" name="z_dataframe" />
            <output file="global.pdf" ftype="pdf" name="pdf" />
        </test>

        <test>
            <param ftype="bam" name="input" value="sr_bowtie.bam" />
            <param name="minquery" value="23" />
            <param name="maxquery" value="29" />
            <param name="mintarget" value="23" />
            <param name="maxtarget" value="29" />
            <param name="minscope" value="5" />
            <param name="maxscope" value="15" />
            <conditional name="plot_options">
                <param name="plot_method" value="global" />
            </conditional>
            <param name="npairs_ylim" value="100" />
            <param name="npairszscore_ylim" value="0" />
            <param name="overlapprob_ylim" value="1" />
            <param name="overlapprobzscore_ylim" value="4" />

            <output file="h.tab" ftype="tabular" name="h_dataframe" />
            <output file="z.tab" ftype="tabular" name="z_dataframe" />
            <output file="global-limited.pdf" ftype="pdf" name="pdf" />
        </test>

        <test>
            <param ftype="bam" name="input" value="sr_bowtie.bam" />
            <param name="minquery" value="23" />
            <param name="maxquery" value="29" />
            <param name="mintarget" value="23" />
            <param name="maxtarget" value="29" />
            <param name="minscope" value="5" />
            <param name="maxscope" value="15" />
            <conditional name="plot_options">
                <param name="plot_method" value="lattice" />
            </conditional>
            <output file="h.tab" ftype="tabular" name="h_dataframe" />
            <output file="z.tab" ftype="tabular" name="z_dataframe" />
            <output file="lattice.pdf" ftype="pdf" name="pdf" />
        </test>
    </tests>