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1 <tool id="Detect_Indels_docker" name="Detect_Indels">
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2 <description> Detect InDels </description>
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3 <requirements>
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4 <container type="docker">takakoron/detect_indel</container>
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5 </requirements>
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6 <command interpreter="perl">
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7 /usr/src/myapp/kick_detect_indels.pl $how.how_specify
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8
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9 #if $how.how_specify == "pileup":
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10 $how.pileup
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11 $how.consensus
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12 $how.snp
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13 $how.map
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14 $how.coverage
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15 $how.het_hom_both
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16 $output1
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17 #else:
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18 $how.mpileup
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19 $how.dp
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20 $how.mq
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21 $how.het_hom_both
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22 $how.gq
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23 $output1
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24 #end if
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25 </command>
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26
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27 <inputs>
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28 <conditional name="how">
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29 <param name="how_specify" type="select" label="Select pileup or mpileup " >
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30 <option value="mpileup">mpileup</option>
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31 <option value="pileup">pileup</option>
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32 </param>
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33 <when value="pileup">
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34 <param name="pileup" type="data" label="Select DNA polymorphism file(format : samtools pileup)" />
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35 <param name="consensus" area="true" type="integer" size="1x10" value="0" label="Consensus quality threshold in pileup file (default: 0)" />
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36 <param name="snp" area="true" type="integer" size="1x10" value="20" label="SNP quality threshold in pileup file (default: 20)" />
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37 <param name="map" area="true" type="integer" size="1x10" value="0" label="Maximum mapping quality threshold in pileup file (default: 0)" />
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38 <param name="coverage" area="true" type="integer" size="1x10" value="8" label="read coverage threshold in pileup file (default: 8)" />
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39 <param name="het_hom_both" type="select" label="Select hets, homs or both (default: both)" >
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40 <option value="both">both</option>
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41 <option value="homs">homs</option>
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42 <option value="hets">hets</option>
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43 </param>
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44 </when>
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45 <when value="mpileup">
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46 <param name="mpileup" type="data" label="Select DNA polymorphism file(format : samtools mpileup)" />
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47 <param name="dp" area="true" type="integer" size="1x10" value="0" label="(DP) Raw read depth threshold in mpileup file (default: 0)" />
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48 <param name="mq" area="true" type="integer" size="1x10" value="0" label="(MQ) Root-mean-square mapping quality threshold in mpileup file (default: 0)" />
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49 <param name="het_hom_both" type="select" label="(GT) Select hets, homs or both (default: both)" >
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50 <option value="both">both</option>
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51 <option value="homs">homs</option>
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52 <option value="hets">hets</option>
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53 </param>
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54 <param name="gq" area="true" type="integer" size="1x10" value="0" label="(GQ) Genotype quality threshold in mpileup file (default: 0)" />
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55 </when>
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56 </conditional>
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57 </inputs>
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58
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59 <outputs>
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60 <data name="output1" label="InDels data" type="data" format="vcf"/>
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61 </outputs>
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62
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63 <!---
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64 <help>
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65
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66 .. class:: infomark
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67 **About data**
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68
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69 Distribution of chromosome is appeared in order of genome file.
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70
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71 </help>
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72 -->
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73
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74 </tool>
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75
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76
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