view MiClip.xml @ 101:4235fcb5b090 draft

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<tool id="mi_clip" name="MiClip">
    <description>Identify Binding Sites in CLIP-Seq Data</description>
    <requirements>
        <requirement type="binary">Rscript</requirement>
        <requirement type="package" version="3.0.1">R_3_0_1</requirement>
        <requirement type="package" version="1.2">miclip</requirement>
        <requirement type="package" version="5.18.1">perl</requirement>
        <requirement type="set_environment">MICLIP_SCRIPT_PATH</requirement>
    </requirements>
    <command interpreter="sh">
        MiClip_wrapper.sh $input_file $control_file $mutation $paired $suffix $step $maxbin $model_cut $max_iter $convergence $emperical $output
    </command>
    <inputs>
        <param name="input_file" type="data" format="sam" label="Input File" help="Input SAM File. Use Bam to Sam converter if Input file is in Bam format."/>
        <param name="control_file" type="data" format="sam" optional="true" label="Control File" help="ex: Control experiment without crosslinking for distinguishing SNPs."/> 
        <param name="mutation" type="select" label="Mutation Type" display="checkboxes" multiple="true" help="Select One or Multiple Mutations.">
            <option value="T2C" selected="true">T-&gt;C</option>
            <option value="T2A">T-&gt;A</option>
            <option value="T2G">T-&gt;G</option>
            <option value="C2A">C-&gt;A</option>
            <option value="C2T">C-&gt;T</option>
            <option value="C2G">C-&gt;G</option>
            <option value="A2T">A-&gt;T</option>
            <option value="A2G">A-&gt;G</option>
            <option value="A2C">A-&gt;C</option>
            <option value="G2A">G-&gt;A</option>
            <option value="G2C">G-&gt;C</option>
            <option value="G2T">G-&gt;T</option>
            <option value="Ins">Ins</option>
            <option value="Del">Del</option>
        </param>

        <param name="paired" type="boolean" checked="no" truevalue="TRUE" falsevalue="FALSE" label="Sequence is Pair-End" help=""/>
        <param name="suffix" type="text" size="20" value="Forward,Backward" label="Suffix of Paired-End Read" help="Change only if Paired-End Reads. See Manual for more details."/>
        <param name="step" type="integer" value="5" label="Bin Step Size" help="In the first HMM, all clusters will be divided into bins of the same length of step bp."/>
        <param name="maxbin" type="integer" value="100" label="Max Number of Reads per Bin" help="Maximum number of Reads in a Bin or on a Base."/>
        <param name="emperical" type="text" value="auto" label="Emperical" help="Used in model fitting in the first HMM. Default is 'auto'."/> 
        <param name="model_cut" type="float" value="0.2" min="0.0" max="1.0" label="Mixure Model Cutoff" help="Cutoff for Fitting the mixture model in the Second HMM."/>
        <param name="max_iter" type="integer" value="20" label="Max Number of HMM Iterations" help="The Maximum number of Iterations for both HMM iterations."/>
        <param name="convergence" type="float" value="0.01" label="Convergence Cutoff" help="The Cutoff for reaching Convergence."/>
    </inputs>
    <outputs>
        <data format="zip" name="output" />
    </outputs>
    <help>

**Description**

Cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-Seq) has made it possible to identify targeting sites of RNA-binding proteins in various cell culture systems and tissue types on a genome-wide scale. Here we present MiClip,a novel model-based approach to identify high-confidence protein-RNA binding sites in CLIP-Seq datasets. This approach assigns confidence value to each binding site on a probabilistic basis. The MiClip package can be flexibly applied to analyze both HITS-CLIP data and PAR-CLIP data. 


------

**Manual**
GalaxyManual_

.. _GalaxyManual: http://galaxy.swmed.edu/galaxy/static/galaxy_manual.pdf

MiniClipDemo_

.. _MiniClipDemo: http://galaxy.swmed.edu/galaxy/u/tpers1/p/miniclipwalkthrough

Vignette.pdf_ 

.. _Vignette.pdf: http://galaxy.swmed.edu/galaxy/static/MiClip_vignette.pdf

Manual.pdf_ 

.. _Manual.pdf: http://galaxy.swmed.edu/galaxy/static/MiClip-manual.pdf


------

**Source**

MiClip_R_Package_

.. _MiClip_R_Package: http://galaxy.swmed.edu/galaxy/static/MiClip.tar.gz

------

**Author** 

Tao Wang. 
For any suggestions or inquiries please contact [e-mail]


    </help>
</tool>