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1 <tool id="methyation_by_region_tool" name="Methylation by Region Converter" version="0.1.1">
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2 <description>: create a bedgrapgh with methylation percentages aggregated by region</description>
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3 <requirements>
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4 <requirement type="package" version="0.1.16">samtools</requirement>
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5 <requirement type="package" version="0.12.7">bowtie2</requirement>
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6 </requirements>
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7 <command interpreter="perl">
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8
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9 methylation_by_region_converter.pl
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10
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11 -o $output
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12 -l $summary
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13 ## Handle reference file.
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14 #if $refBedSource.bedSource == "history":
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15 $refBedSource.ownFile
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16 #else:
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17 "${refBedSource.index.fields.path}"
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18 #end if
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19 $bedgraph
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20
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21 </command>
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22 <inputs>
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23 <conditional name="refBedSource">
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24 <param name="bedSource" type="select" label="Will you select a bed file from your history or use a built-in one?" help="Built-ins were created using default options">
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25 <option value="indexed">Use a built-in index</option>
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26 <option value="history">Use one from the history</option>
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27 </param>
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28 <when value="indexed">
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29 <param name="index" type="select" label="Select a bed file" help="If bed file is not listed, contact the Galaxy team">
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30 <options from_data_table="bismark_bed_files">
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31 <filter type="sort_by" column="1"/>
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32 <validator type="no_options" message="No files are available for the selected input dataset"/>
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33 </options>
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34 </param>
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35 </when>
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36 <when value="history">
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37 <param name="ownFile" type="data" format="bed" metadata_name="dbkey" label="Select the bed file" />
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38 </when> <!-- history -->
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39 </conditional> <!-- refGenomeSource -->
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40 <param name="bedgraph" type="data" format="bedgraph" label="BedGraph file" />
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41 <param name="sample" type="text" label="Sample Name" />
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42
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43 </inputs>
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44 <outputs>
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45 <data name="output" format="tabular" label="${tool.name} on ${on_string}" />
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46 <data name="summary" format="txt" label="${tool.name} summary" />
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47 </outputs>
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48 <help>
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49 |
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50
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51
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52 **What it does**
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53
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54
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55 Script to take a bed file of target regions and a series of bedgraphs from bismark and create a bedgrapgh with methylation percentages aggregated by region
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56
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57
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58 -----
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59
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60
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61 ::
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62
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63 Usage: methylation_by_region_converter.pl [OPTIONS] bed_file bedGraph
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64
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65
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66 </help>
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67 </tool>
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68
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69
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