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1 <tool id="bismark_meth_caller" name="Bismark Methylation Caller">
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2 <requirements>
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3 <requirement type="package">
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4 Bismark
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5 </requirement>
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6 </requirements>
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7 <command interpreter="bash">
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8 bismark_meth_caller.sh
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9 input=$bismark_sam
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10 method=$single_paired
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11 output=$output
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12 tempdir=$output.files_path
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13
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14 </command>
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15 <inputs>
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16 <param name="single_paired" type="select" label="Please select whether Reads are single-end or paired-end">
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17 <option value="s">Single-end</option>
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18 <option value="p">Paired-end</option>
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19 </param>
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20 <param format="sam" name="bismark_sam" type="data" label="Bismark mapping output file" help="Must be in SAM format"/>
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21 </inputs>
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22 <outputs>
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23 <data name="output" format ="bed" label="Bismark methylation output" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="bismark_sam" value="bismark_mapped_reads_single.sam" ftype="sam"/>
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28 <param name="single_paired" value="s"/>
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29 <output name="output" file="bismark_methylation_output_single.bed"/>
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30 </test>
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31 <test>
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32 <param name="bismark_sam" value="bismark_mapped_reads_single.sam" ftype="sam"/>
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33 <param name="single_paired" value="p"/>
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34 <output name="output" file="bismark_methylation_output_paired.bed"/>
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35 </test>
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36 </tests>
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37 <help>
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38 **What it does**
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39
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40 This methylation caller parses the Bismark SAM output file into bed format. You only need to specify whether the reads are single-end or paired-end
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41
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42
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43 **Output format** ::
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44
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45
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46 Column Description
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47 ---------------------- --------------------------------------
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48 1 chr chromosome
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49 2 pos position
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50 3 strand strand
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51 4 context context (CHH,CHG,CpG)
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52 5 coverage totally sequenced Cs at that position
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53 6 methylated methylated Cs at that position
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54 7 percentage methylated percentage of 6
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55 </help>
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56 </tool>
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57
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