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101
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1 <tool id="mi_clip" name="MiClip">
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2 <description>Identify Binding Sites in CLIP-Seq Data</description>
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3 <requirements>
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4 <requirement type="binary">Rscript</requirement>
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5 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
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6 <requirement type="package" version="1.2">miclip</requirement>
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7 <requirement type="package" version="5.18.1">perl</requirement>
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8 <requirement type="set_environment">MICLIP_SCRIPT_PATH</requirement>
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9 </requirements>
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10 <command interpreter="sh">
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11 MiClip_wrapper.sh $input_file $control_file $mutation $paired $suffix $step $maxbin $model_cut $max_iter $convergence $emperical $output
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12 </command>
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13 <inputs>
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14 <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."/>
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15 <param name="control_file" type="data" format="sam" optional="true" label="Control File" help="ex: Control experiment without crosslinking for distinguishing SNPs."/>
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16 <param name="mutation" type="select" label="Mutation Type" display="checkboxes" multiple="true" help="Select One or Multiple Mutations.">
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17 <option value="T2C" selected="true">T->C</option>
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18 <option value="T2A">T->A</option>
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19 <option value="T2G">T->G</option>
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20 <option value="C2A">C->A</option>
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21 <option value="C2T">C->T</option>
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22 <option value="C2G">C->G</option>
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23 <option value="A2T">A->T</option>
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24 <option value="A2G">A->G</option>
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25 <option value="A2C">A->C</option>
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26 <option value="G2A">G->A</option>
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27 <option value="G2C">G->C</option>
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28 <option value="G2T">G->T</option>
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29 <option value="Ins">Ins</option>
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30 <option value="Del">Del</option>
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31 </param>
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32
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33 <param name="paired" type="boolean" checked="no" truevalue="TRUE" falsevalue="FALSE" label="Sequence is Pair-End" help=""/>
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34 <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."/>
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35 <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."/>
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36 <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."/>
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37 <param name="emperical" type="text" value="auto" label="Emperical" help="Used in model fitting in the first HMM. Default is 'auto'."/>
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38 <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."/>
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39 <param name="max_iter" type="integer" value="20" label="Max Number of HMM Iterations" help="The Maximum number of Iterations for both HMM iterations."/>
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40 <param name="convergence" type="float" value="0.01" label="Convergence Cutoff" help="The Cutoff for reaching Convergence."/>
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41 </inputs>
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42 <outputs>
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43 <data format="zip" name="output" />
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44 </outputs>
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45 <help>
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46
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47 **Description**
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48
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49 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.
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50
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51
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52 ------
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53
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54 **Manual**
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55 GalaxyManual_
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56
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57 .. _GalaxyManual: http://galaxy.swmed.edu/galaxy/static/galaxy_manual.pdf
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58
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59 MiniClipDemo_
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60
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61 .. _MiniClipDemo: http://galaxy.swmed.edu/galaxy/u/tpers1/p/miniclipwalkthrough
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62
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63 Vignette.pdf_
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64
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65 .. _Vignette.pdf: http://galaxy.swmed.edu/galaxy/static/MiClip_vignette.pdf
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66
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67 Manual.pdf_
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68
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69 .. _Manual.pdf: http://galaxy.swmed.edu/galaxy/static/MiClip-manual.pdf
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70
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71
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72 ------
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73
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74 **Source**
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75
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76 MiClip_R_Package_
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77
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78 .. _MiClip_R_Package: http://galaxy.swmed.edu/galaxy/static/MiClip.tar.gz
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79
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80 ------
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81
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82 **Author**
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83
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84 Tao Wang.
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85 For any suggestions or inquiries please contact Tao.Wang@UTSouthwestern.edu
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86
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87
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88 </help>
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89 </tool>
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