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<?xml version="1.0" encoding="utf-8"?>
<tool id="metilene" name="metilene" version="0.2-4.4">
    <description>
        calling differentially methylated regions from
        bisulfite sequencing data
    </description>
    
    <requirements>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="5.18.1" >perl</requirement>
        <requirement type="package" version="3.2.1" >R</requirement>
        <requirement type="package" version="2.24" >bedtools</requirement>
        <requirement type="package" version="0.2-4" >metilene</requirement>
        <requirement type="package" version="8.22">gnu_coreutils</requirement>
    </requirements>
    
    <stdio>
        <exit_code range=":-1"/>
        <exit_code range="1:" />
    </stdio>

    <version_command>echo "0.2-4"</version_command>

    <command><![CDATA[
    ## =============== preprocessing
    ##   generate metilene_g1_g2.input from multiple bedgraph files
    metilene_input.pl 
    --in1 $opt_in1
    ##echo ",".join(map(str,$opt_in1))
    --in2 $opt_in2
    ##echo ",".join(map(str,$opt_in2))
    >/dev/null 2>/dev/null
    ;
    ## ===============  metilene main program
    metilene 
    -M $Options.opt_M -m $Options.opt_m -d $Options.opt_d -t 1 -f 1 -v $Options.opt_v
    metilene_g1_g2.input
    >$output_bedlike
    2>/dev/null
    ;
    ## =============== postprocessing
    cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null
    ;
    ## write to job directory ...
    metilene_output.pl -q $output_bedlike -p 0.05 -o ./metilene >/dev/null 2>/dev/null
    ;
    ## ... and move to output files
    mv metilene_qval.0.05.bedgraph $output_qval_bedgraph 2>/dev/null;
    mv metilene_qval.0.05.out $output_qval_out 2>/dev/null;
    mv metilene_qval.0.05.pdf $output_qval_pdf 2>/dev/null
    ]]></command>
    
    <inputs>
        <!-- input bedgraph files 1 -->
        <param
            name="opt_in1"
            type="data" format="bed,bedgraph" multiple="true"
            optional="false"
            label="Input group 1"
            help="set of sorted bedgraph input profiles of group 1" />
        <!-- input bedgraph files 2 -->
        <param
            name="opt_in2"
            type="data" format="bed,bedgraph" multiple="true"
            optional="false"
            label="Input group 2"
            help="set of sorted bedgraph input profiles of group 2" />
        
        <!-- Advanced parameters (folded) -->
        <section name="Options" title="Advanced Options" expanded="False">
	    <param
                name="opt_M" 
                label="The allowed nt distance between two CpGs within a DMR"
                type="integer"
	        optional="false"
                value="300"
	        help="-M, --maxdist"/>

            <param
                name="opt_m" 
                label="The minimum # of CpGs in a DMR"
                type="integer"
	        optional="false"
                value="10"
	        help="-m, --mincpgs"/>
            
            <param
                name="opt_d" 
                label="The minimum mean methylation difference for calling DMRs"
                type="float"
	        optional="false"
                value="0.1"
	        help="-d, --minMethDiff"/>

            <param
                name="opt_v" 
                label="Stringency of the valley filter (0.0 - 1.0)"
                type="float"
	        optional="false"
                value="0.7"
	        help="-v, --valley">
                <validator type="in_range" min="0.0" max="1.0" 
                           message="Valley filter value must be in [0,1]." />
            </param>    
	</section>
    </inputs>
    
    <outputs>
        <!-- finally: for bed-like use format=tabular -->
        <data format="tabular" name="output_bedlike" 
              label="${tool.name} on ${on_string}" />
        <data format="bedgraph" name="output_bedgraph" 
              label="${tool.name} on ${on_string}" />
        <data format="bedgraph" name="output_qval_bedgraph" 
              label="${tool.name} qval&lt;0.05 bedgraph on ${on_string}" />
        <data format="pdf" name="output_qval_pdf" 
              label="${tool.name} qval&lt;0.05 plots on ${on_string}" />
        <data format="bedgraph" name="output_qval_out" 
              label="${tool.name} qval&lt;0.05 out on ${on_string}" />
    </outputs>
    
    <tests>
        <test>
	    <param name="opt_in1" value="example_S1.bedgraph,example_S2.bedgraph,example_S3.bedgraph,example_S4.bedgraph" />
            <param name="opt_in2" value="example_S5.bedgraph,example_S6.bedgraph,example_S7.bedgraph,example_S8.bedgraph" />
	    <output name="output_bedlike" file="metilene.out" />
        </test>
    </tests>
    
    
    <help><![CDATA[
**Fast and sensitive calling of differentially methylated regions
from bisulfite sequencing data**

Detailed documentation of the stand-alone tool metilene is available at
.. __: http://www.bioinf.uni-leipzig.de/Software/metilene/manual.pdf

The software metilene is available for download at
.. __: http://www.bioinf.uni-leipzig.de/Software/metilene/
    ]]></help>

    <citations>
        <citation type="bibtex">@Article{Juhling_Kretzmer_Bernhart-metil_Fast_and-2015,
  author =	 {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan 
                  H. and Otto, Christian and Stadler, Peter F. and Hoffmann, 
                  Steve},
  title =	 {metilene: {Fast} and sensitive calling of differentially 
                  methylated regions from bisulfite sequencing data},
  page =         {[Epub ahead of print]},
  journal =	 {Genome Res},
  year =	 {2015},
  pmid =	 {26631489},
  doi = 	 {10.1101/gr.196394.115},
  issn = 	 {1088-9051},
  issn = 	 {1549-5469}}</citation>
    </citations>
    
</tool>