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annotate pilon.cwl @ 1:ee888e5fe28f draft

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planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit fc0659094c338f551b09bd2ba314fe06d7024f33
author sanbi-uwc
date Thu, 11 Aug 2016 08:23:08 -0400
parents eaf4a7ae3a8f
children
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rev   line source
0
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
sanbi-uwc
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1 #!/usr/bin/env cwl-runner
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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2
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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3 cwlVersion: v1.0
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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4 class: CommandLineTool
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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5 stdout: output.txt
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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6
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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7 requirements:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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8 - class: EnvVarRequirement
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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9 envDef:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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10 - envName: CLASSPATH
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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11 envValue: /home/pvh/Documents/code/SANBI/pilon/pilon-1.18.jar
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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12 # - class: InlineJavascriptRequirement
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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13
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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14 inputs:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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15 java_opts:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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16 type: string?
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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17 doc: "JVM arguments should a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")"
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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18 inputBinding:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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19 position: 1
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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20 genome:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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21 type: File
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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22 doc: |
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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23 The input genome we are trying to improve, which must be the reference used
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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24 for the bam alignments. At least one of --frags or --jumps must also be given.
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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25 inputBinding:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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26 position: 5
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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27 prefix: "--genome"
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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28 frags:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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29 type:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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30 - 'null'
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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31 - type: array
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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32 items: File
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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33 inputBinding:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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34 prefix: --frags
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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35 position: 6
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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36 doc: |
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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37 A bam file consisting of fragment paired-end alignments, aligned to the --genome
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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38 argument using bwa or bowtie2. This argument may be specifed more than once.
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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39 secondaryFiles:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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40 - ".bai"
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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41 jumps:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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42 type:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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43 - 'null'
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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44 - type: array
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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45 items: File
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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46 inputBinding:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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47 prefix: --jumps
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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48 position: 6
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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49 doc: |
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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50 A bam file consisting of fragment paired-end alignments, aligned to the --genome
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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51 argument using bwa or bowtie2. This argument may be specifed more than once.
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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52 secondaryFiles:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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53 - ".bai"
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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54 unpaired:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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55 type:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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56 - 'null'
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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57 - type: array
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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58 items: File
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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59 inputBinding:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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60 prefix: --unpaired
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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61 position: 6
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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62 doc: |
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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63 A bam file consisting of unpaired alignments, aligned to the --genome argument
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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64 using bwa or bowtie2. This argument may be specifed more than once.
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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65 secondaryFiles:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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66 - ".bai"
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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67 bam:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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68 type:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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69 - 'null'
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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70 - type: array
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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71 items: File
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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72 inputBinding:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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73 prefix: "--bam"
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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74 position: 6
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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75 secondaryFiles:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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76 - ".bai"
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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77 doc: |
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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78 A bam file of unknown type; Pilon will scan it and attempt to classify it as one
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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79 of the above bam types.
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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80 vcf_output:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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81 type: boolean
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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82 default: false
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83 inputBinding:
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sanbi-uwc
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84 position: 7
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sanbi-uwc
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85 prefix: "--vcf"
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86 output_prefix:
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87 type: string
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88 default: pilon
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89 inputBinding:
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90 prefix: "--output"
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sanbi-uwc
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91 position: 7
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92 variant_output:
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sanbi-uwc
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93 type: boolean
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sanbi-uwc
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94 default: false
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sanbi-uwc
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95 doc: Sets up heuristics for variant calling, as opposed to assembly improvement, equivalent to "--vcf --fix all,breaks"
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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96 inputBinding:
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97 prefix: --variant
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98 position: 7
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sanbi-uwc
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99 changes:
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sanbi-uwc
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100 type: boolean
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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101 default: false
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102 doc: Output file describing changes in FASTA output
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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103 inputBinding:
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104 prefix: --changes
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105 position: 7
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sanbi-uwc
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106 tracks:
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sanbi-uwc
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107 type: boolean
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108 default: false
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109 doc: Write many track files (*.bed, *.wig) suitable for viewing in a genome browser.
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110 inputBinding:
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sanbi-uwc
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111 prefix: --tracks
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112 position: 7
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113 vcfqe:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
sanbi-uwc
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114 type: boolean
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
sanbi-uwc
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115 default: false
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116 doc: Add a QE (quality-weighted evidence) field rather than the default QP (quality-weighted percentage of evidence) field.
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117 inputBinding:
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118 prefix: --vcfqe
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sanbi-uwc
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119 position: 7
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120 chunksize:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
sanbi-uwc
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121 type: int?
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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122 doc: Input FASTA elements larger than this will be processed in smaller pieces not to exceed this size (default 10000000).
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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123 inputBinding:
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sanbi-uwc
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124 prefix: --chunksize
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sanbi-uwc
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125 position: 8
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126 vcf:
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127 type: boolean
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128 default: false
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129 doc: Generate a VCF file describing variants
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130 inputBinding:
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131 prefix: --vcf
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132 position: 8
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133 diploid:
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134 type: boolean
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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135 default: false
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sanbi-uwc
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136 doc: Sample is from diploid organism; will eventually affect calling of heterozygous SNPs
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137 inputBinding:
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138 prefix: --diploid
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139 position: 8
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140 fix:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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141 type: string?
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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142 doc: |
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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143 A comma-separated list of categories of issues to try to fix:
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144 "bases": try to fix individual bases and small indels;
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145 "gaps": try to fill gaps;
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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146 "local": try to detect and fix local misassemblies;
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147 "all": all of the above (default);
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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148 "none": none of the above; new fasta file will not be written.
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149 The following are experimental fix types:
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150 "amb": fix ambiguous bases in fasta output (to most likely alternative).
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151 "breaks": allow local reassembly to open new gaps (with "local").
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152 "novel": assemble novel sequence from unaligned non-jump reads.
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153 inputBinding:
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154 prefix: --fix
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155 position: 8
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156 dumpreads:
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157 type: boolean
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158 default: false
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159 doc: Dump reads for local re-assemblies.
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160 inputBinding:
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161 prefix: --dumpreads
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162 position: 8
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163 duplicates:
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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164 type: boolean
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165 default: false
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166 doc: Use reads marked as duplicates in the input BAMs (ignored by default).
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167 inputBinding:
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168 prefix: --duplicates
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169 position: 8
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diff changeset
170 iupac:
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171 type: boolean
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172 default: false
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173 doc: Output IUPAC ambiguous base codes in the output FASTA file when appropriate.
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174 inputBinding:
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175 prefix: --iupac
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176 position: 8
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177 nonpf:
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178 type: boolean
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179 default: false
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180 doc: Use reads which failed sequencer quality filtering (ignored by default).
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181 inputBinding:
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182 prefix: --nonpf
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183 position: 8
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184 targets:
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185 type: string?
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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186 doc: |
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187 Only process the specified target(s). Targets are comma-separated, and each target
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188 is a fasta element name optionally followed by a base range.
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189 Example: "scaffold00001,scaffold00002:10000-20000" would result in processing all of
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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190 scaffold00001 and coordinates 10000-20000 of scaffold00002.
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191 If "targetlist" is the name of a file, each line will be treated as a target
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192 specification.
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193 inputBinding:
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194 prefix: --targets
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195 position: 8
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196 threads:
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197 type: int?
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198 doc: Degree of parallelism to use for certain processing (default 1). Experimental.
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199 default: 1
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200 inputBinding:
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201 prefix: --threads
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202 position: 8
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203 verbose:
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204 type: boolean
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205 default: false
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206 doc: More verbose output
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207 inputBinding:
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208 prefix: --verbose
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209 position: 8
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210 debug:
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211 type: boolean
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212 default: false
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213 doc: Debugging output (implies verbose)
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214 inputBinding:
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215 prefix: --debug
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216 position: 8
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217 defaultqual:
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218 type: int?
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219 doc: Assumes bases are of this quality if quals are no present in input BAMs (default 15).
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220 inputBinding:
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221 prefix: --defaultqual
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222 position: 9
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223 flank:
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224 type: int?
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225 doc: Controls how much of the well-aligned reads will be used; this many bases at each end of the good reads will be ignored (default 10).
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226 inputBinding:
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227 prefix: --flank
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228 position: 9
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229 gapmargin:
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230 type: int?
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231 doc: Closed gaps must be within this number of bases of true size to be closed (100000)
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232 inputBinding:
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233 prefix: --gapmargin
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234 position: 9
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235 kmersize:
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236 type: int?
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237 doc: Kmer size used by internal assembler (default 47).
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238 inputBinding:
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239 prefix: --K
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240 position: 9
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241 mindepth:
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242 type: float?
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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243 doc: |
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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244 Variants (snps and indels) will only be called if there is coverage of good pairs
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245 at this depth or more; if this value is >= 1, it is an absolute depth, if it is a
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246 fraction < 1, then minimum depth is computed by multiplying this value by the mean
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247 coverage for the region, with a minumum value of 5 (default 0.1: min depth to call
eaf4a7ae3a8f planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/pilon commit 24ff006e6dae824c9cb9aeb6dfd04bfb624cdd3e
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248 is 10% of mean coverage or 5, whichever is greater).
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249 inputBinding:
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250 prefix: --mindepth
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251 position: 9
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252 mingap:
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253 type: int?
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254 doc: Minimum size for unclosed gaps (default 10)
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255 inputBinding:
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256 prefix: --mingap
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257 position: 9
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258 minmq:
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259 type: int?
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260 doc: Minimum alignment mapping quality for a read to count in pileups (default 0)
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261 inputBinding:
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262 prefix: --minmq
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263 position: 9
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264 minqual:
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265 type: int?
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266 doc: Minimum base quality to consider for pileups (default 0)
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267 inputBinding:
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268 prefix: --minqual
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269 position: 9
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270 nostrays:
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271 type: boolean
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272 default: false
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273 doc: |
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274 Skip making a pass through the input BAM files to identify stray pairs, that is,
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275 those pairs in which both reads are aligned but not marked valid because they have
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276 inconsistent orientation or separation. Identifying stray pairs can help fill gaps
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277 and assemble larger insertions, especially of repeat content. However, doing so
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278 sometimes consumes considerable memory.
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279 inputBinding:
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280 prefix: --nostrays
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281 position: 9
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282
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283 outputs:
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284 pilon_output:
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285 type: stdout
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286 fasta_output:
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287 type: File?
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288 outputBinding:
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289 glob: $(inputs.output_prefix).fasta
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290 vcf_output:
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291 type: File?
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292 outputBinding:
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293 glob: $(inputs.output_prefix).vcf
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294 track_outputs:
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295 type: File[]?
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296 outputBinding:
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297 glob:
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298 - $(inputs.output_prefix)Pilon.bed
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299 - $(inputs.output_prefix)Changes.wig
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300 - $(inputs.output_prefix)Unconfirmed.wig
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301 - $(inputs.output_prefix)CopyNumber.wig
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302 - $(inputs.output_prefix)Coverage.wig
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303 - $(inputs.output_prefix)BadCoverage.wig
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304 - $(inputs.output_prefix)PctBad.wig
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305 - $(inputs.output_prefix)DeltaCoverage.wig
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306 - $(inputs.output_prefix)DipCoverage.wig
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307 - $(inputs.output_prefix)PhysicalCoverage.wig
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308 - $(inputs.output_prefix)ClippedAlignments.wig
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309 - $(inputs.output_prefix)WeightedQual.wig
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310 - $(inputs.output_prefix)WeightedMq.wig
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311 - $(inputs.output_prefix)GC.wig
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312
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313 changes_output:
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314 type: File?
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315 outputBinding:
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316 glob: $(inputs.output_prefix).changes
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317
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318 baseCommand: [java]
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319
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320 arguments:
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321 - valueFrom: "com.simontuffs.onejar.Boot"
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322 position: 2
1
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323
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324 doc: |
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325 Pilon is a software tool which can be used to:
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326
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327 * Automatically improve draft assemblies
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328 * Find variation among strains, including large event detection
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329
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330 For more info: https://github.com/broadinstitute/pilon/wiki