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1 <tool id="covacs_mpileup" name="covacs_mpileup" version="1.9">
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2 <description>samtools mpileup wrapper for covacs</description>
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3 <macros>
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4 <import>bed_macros.xml</import>
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5 <import>covacs_macros.xml</import>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="1.9" >samtools</requirement>
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9 </requirements>
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10 <command>
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11 <![CDATA[
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12
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13
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14 samtools mpileup
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15 -C $adjust
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16 #if $bed_source.bed_source_selector == "history" and $bed_source.bed_history
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17 -l $bed_source.bed_history
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18 #end if
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19 #if $bed_source.bed_source_selector == "cached"
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20 -l $bed_source.bed_cached.fields.path
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21 #end if
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22
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23 -d $depth
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24 -q $MappingQuality
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25 -Q $BaseQuality
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26 #if $reference_source.reference_source_selector == "cached"
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27 -f $reference_source.ref_file.fields.path
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28 #end if
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29
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30 #if $reference_source.reference_source_selector == "history"
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31
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32 -f $reference_source.ref_file_h
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33
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34 #end if
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35
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36 $input1 -A -o $output 2>$log
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37
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38
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39
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40
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41
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42 ]]>
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43 </command>
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44 <inputs>
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45 <param format="bam" name="input1" label="bam-input" type="data" optional="true" />
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46 <param name="adjust" type="integer" optional="true" value="50" help="adjust mapping quality"/>
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47 <expand macro="bed_loc"/>
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48 <param name="depth" type="integer" optional="true" value="100000" help="max per-file depth" />
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49 <param name="MappingQuality" type="integer" optional="true" value="0" help="skip alignments with mapQ smaller than INT" />
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50 <param name="BaseQuality" type="integer" optional="true" value="0" help="skip bases with baseQ/BAQ smaller than INT" />
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51 <expand macro="reference_loc"/>
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52 </inputs>
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53 <outputs>
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54 <data format="pileup" name="output" label="mpileup on ${on_string}"/>
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55 <data format="txt" name="log" label="mpileup on ${on_string}:log"/>
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56 </outputs>
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57 <help>
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58 **more information** at http://www.htslib.org/doc/samtools-1.2.html
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59
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60 **Implemented options** samtools mpileup
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61 -B, --no-BAQ disable BAQ (per-Base Alignment Quality)
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62 -C, --adjust-MQ INT adjust mapping quality; recommended:50, disable:0 [0]
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63 -d, --max-depth INT max per-file depth; avoids excessive memory usage [8000]
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64 -f, --fasta-ref FILE faidx indexed reference sequence file
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65 -l, --positions FILE skip unlisted positions (chr pos) or regions (BED)
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66 -q, --min-MQ INT skip alignments with mapQ smaller than INT [0]
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67 -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [13]
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68 **fixed option**
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69 -A, --count-orphans do not discard anomalous read pairs
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70
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71 </help>
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72 <citations>
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73 <citation type="doi">10.1186/s12864-018-4508-1</citation>
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74 </citations>
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75 </tool>
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76
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