Mercurial > repos > bgruening > upload_testing
diff MiClip.xml @ 101:4235fcb5b090 draft
Uploaded
| author | bgruening |
|---|---|
| date | Sun, 02 Mar 2014 11:49:08 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MiClip.xml Sun Mar 02 11:49:08 2014 -0500 @@ -0,0 +1,89 @@ +<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->C</option> + <option value="T2A">T->A</option> + <option value="T2G">T->G</option> + <option value="C2A">C->A</option> + <option value="C2T">C->T</option> + <option value="C2G">C->G</option> + <option value="A2T">A->T</option> + <option value="A2G">A->G</option> + <option value="A2C">A->C</option> + <option value="G2A">G->A</option> + <option value="G2C">G->C</option> + <option value="G2T">G->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 Tao.Wang@UTSouthwestern.edu + + + </help> +</tool>