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annotate unicycler.xml @ 0:15a21071f0a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
author iuc
date Thu, 06 Jul 2017 17:07:27 -0400
parents
children 3c7b8504e32a
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15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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1 <tool id="unicycler" name="Create assemblies with Unicycler" version="0.2.0">
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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2 <requirements>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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3 <requirement type="package" version="0.3.0b">unicycler</requirement>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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4 </requirements>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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5 <command detect_errors="exit_code"><![CDATA[
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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7 ## Preparing files
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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8
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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9 #if str( $paired_unpaired.fastq_input_selector ) == "paired":
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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11 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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12 ln -s '${paired_unpaired.fastq_input1}' fq1.fastq &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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13 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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14 ln -s '${paired_unpaired.fastq_input1}' fq1.fastq.gz &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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15 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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17 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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18 ln -s '${paired_unpaired.fastq_input2}' fq2.fastq &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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19 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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20 ln -s '${paired_unpaired.fastq_input1}' fq2.fastq.gz &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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21 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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23 #elif str( $paired_unpaired.fastq_input_selector ) == "paired_collection":
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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25 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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26 ln -s '${paired_unpaired.fastq_input1.forward}' fq1.fastq &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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27 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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28 ln -s '${paired_unpaired.fastq_input1.forward}' fq1.fastq.gz &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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29 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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31 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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32 ln -s '${paired_unpaired.fastq_input1.reverse}' fq2.fastq &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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33 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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34 ln -s '${paired_unpaired.fastq_input2.reverse}' fq2.fastq.gz &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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35 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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36
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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37 #elif str( $paired_unpaired.fastq_input_selector ) == "single":
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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38
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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39 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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40 ln -s '${paired_unpaired.fastq_input1}' fq.fastq &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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41 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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42 ln -s '${paired_unpaired.fastq_input1}' fq.fastq.gz &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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43 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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44
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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45 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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46
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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47 ## Get location for pilon installation
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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48
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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49 pilon=`pilon --jar_dir` &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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50
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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51 #if $long_reads:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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52 #if $long_reads.is_of_type('fastqsanger'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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53 #set lr = "lr.fastq"
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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54 ln -s '${long_reads}' lr.fastq &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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55 #elif $long_reads.is_of_type('fastqsanger.gz'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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56 #set lr = "lr.fastq.gz"
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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57 ln -s '${long_reads}' lr.fastq.gz &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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58 #elif $long_reads.is_of_type('fasta'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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59 #set lr = "lr.fasta"
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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60 ln -s '${long_reads}' lr.fasta &&
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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61 #end if
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62 #end if
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63
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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64 ## Running Unicycler
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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65
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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66 unicycler -t "\${GALAXY_SLOTS:-4}"
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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67
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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68 -o ./
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69 --verbosity 3
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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70 --pilon_path \$pilon
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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71
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72 #if str( $paired_unpaired.fastq_input_selector ) != "single":
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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73
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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74 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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75 -1 fq1.fastq
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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76 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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77 -1 fq1.fastq.gz
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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78 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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79
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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80 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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81 -2 fq2.fastq
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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82 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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83 -2 fq2.fastq.gz
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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84 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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85
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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parents:
diff changeset
86 #else:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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87
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
88 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
89 -s fq.fastq
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
90 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
91 -s fq.fastq.gz
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
92 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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93
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
94 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
95
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
96 #if $long_reads:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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97
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
98 -l $lr
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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99
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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100 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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101
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102 ## General Unicycler Options section
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iuc
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103 ## ----------------------------------------------------------
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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104
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105 --mode '${uc_opt.mode}'
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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106
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iuc
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107 #if $uc_opt.min_fasta_length:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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108 --min_fasta_length $uc_opt.min_fasta_length
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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109 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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110
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iuc
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111 #if $uc_opt.lin_seq:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
112 --expected_linear $uc_opt.lin_seq
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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113 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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114
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115 $uc_opt.no_correct
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116 $uc_opt.no_rotate
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117
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118 ## Rotation Options section
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119 ## ----------------------------------------------------------
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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120
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121 #if $spades.min_kmer_frac:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
122 --min_kmer_frac $spades.min_kmer_frac
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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123 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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124
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iuc
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125 #if $spades.max_kmer_frac:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
126 --max_kmer_frac $spades.max_kmer_frac
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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127 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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128
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iuc
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129 #if $spades.kmer_count:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
130 --kmer_count $spades.kmer_count
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131 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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132
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133 ## Rotation Options section
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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134 ## ----------------------------------------------------------
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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135
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136 #if $rotation.start_genes:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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137 --start_genes '${rotation.rotation_fasta.start_genes}'
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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138 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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139
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iuc
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140 #if $rotation.start_gene_id:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
141 --start_gene_id $rotation.start_gene_id
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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142 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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143
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144 #if $rotation.start_gene_cov:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
145 --start_gene_cov $rotation.start_gene_cov
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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146 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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147
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148 ## Pilon Options section
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149 ## ----------------------------------------------------------
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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150
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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151 #if $pilon.min_polish_size:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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152 --min_polish_size $pilon.min_polish_size
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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153 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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154
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155 ## Graph Cleaning Options sdection
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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156 ## ----------------------------------------------------------
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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157
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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158 #if $graph_clean.min_component_size:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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159 --min_component_size $graph_clean.min_component_size
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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160 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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161 #if $graph_clean.min_dead_end_size:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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162 --min_dead_end_size $graph_clean.min_dead_end_size
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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163 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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164
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165 ## Long Read Alignment Options
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166 ## ----------------------------------------------------------
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167
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168
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169 #if $lr_align.contamination_fasta:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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170 --contamination '${lr_align.contamination_fasta}'
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171 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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172
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173 #if $lr_align.scores:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
174 --scores '${lr_align.scores}'
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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175 #end if
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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176
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177 #if $lr_align.low_score:
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178 --low_score $lr_align.low_score
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179 #end if
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180
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181
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182 ]]></command>
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183
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184 <inputs>
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185 <conditional name="paired_unpaired">
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186 <param name="fastq_input_selector" type="select" label="Paired or Single end data?" help="Select between paired and single end data">
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187 <option selected="True" value="paired">Paired</option>
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188 <option value="paired_collection">Paired Collection</option>
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189 <option value="single">Single</option>
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190 </param>
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191 <when value="paired">
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192 <param name="fastq_input1" argument="-1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
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193 <param name="fastq_input2" argument="-2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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194 </when>
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195 <when value="paired_collection">
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196 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
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197 </when>
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198 <when value="single">
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199 <param name="fastq_input1" argument="-s" type="data" format="fastqsanger,fastqsanger.gz" label="Select unpaired reads" help="Specify dataset with unpaired reads"/>
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200 </when>
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201 </conditional>
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202 <param name="long_reads" argument="--long" optional="True" type="data" format="fastqsanger,fastqsanger.gz,fasta" label="Select long reads. If there are no long reads, leave this empty"/>
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203
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204 <section name="uc_opt" expanded="True" title="Unicycler options">
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205 <param argument="--mode" type="select" label="Select Bridging mode">
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206 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
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207 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
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208 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
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209 </param>
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210 <param argument="--min_fasta_length" optional="True" type="integer" value="" label="Exclude contigs from the FASTA file which are shorter than this length (bp)" help="default = 1"/>
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211 <param argument="--no_correct" optional="True" type="boolean" checked="False" truevalue="--no_correct" falsevalue="" label="Skip SPAdes error correction step" help="This option turns off SPAdes error correction. Generally it is highly recommended to use correction."/>
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212 <param argument="--no_rotate" optional="True" type="boolean" checked="False" truevalue="--no_rotate" falsevalue="" label="Do not rotate completed replicons to start at a standard gene." help="Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence."/>
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213 <param argument="--no_pilon" optional="True" type="boolean" checked="False" truevalue="--no_pilon" falsevalue="" label="Do not use Pilon to polish the final assembly." help="Unicycler uses Pilon tool for polishing final assembly."/>
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214 <param name="lin_seq" argument="--expected_linear_seqs" optional="True" type="integer" value="" label="The expected number of linear (i.e. non-circular) sequences in the assembly" help="default = 0"/>
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215 </section>
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216
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217 <section name="spades" expanded="False" title="SPAdes options" help="Unicycler uses SPAdes to construct assembly graphs. You can modify some of the SPAdes settings here. Use this ONLY if you know what you are doing!">
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218 <param argument="--min_kmer_frac" optional="True" type="float" min="0" max="1" value="" label="Lowest k-mer size for SPAdes assembly, expressed as a fraction of the read length" help="default = 0.2"/>
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219 <param argument="--max_kmer_frac" optional="True" type="float" min="0" max="1" value="" label="Highest k-mer size for SPAdes assembly, expressed as a fraction of the read length" help="default = 0.95"/>
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220 <param argument="--kmer_count" optional="True" type="integer" value="" label="Number of k-mer steps to use in SPAdes assembly" help="default = 10"/>
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221 </section>
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222
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223 <section name="rotation" expanded="False" title="Rotation options" help="These options control the rotation of completed circular sequence near the end of the Unicycler pipeline. Use this ONLY if you know what you are doing!">
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224 <param argument="--start_genes" optional="True" type="data" format="fasta" label="FASTA file of genes for start point of rotated replicons" />
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225 <param argument="--start_gene_id" optional="True" type="integer" min="0" max="100" value="" label="The minimum required BLAST percent identity for a start gene search" help="default = 90"/>
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226 <param argument="--start_gene_cov" optional="True" type="integer" min="0" max="100" value="" label="The minimum required BLAST percent coverage for a start gene search" help="default = 95"/>
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227 </section>
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228
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229 <section name="pilon" title="Pilon options" expanded="False">
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230 <param argument="--min_polish_size" optional="True" type="integer" min="0" label="Contigs shorter than this value (bp) will not be polished using Pilon" help="default = 1000"/>
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231 </section>
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232
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233 <section name="graph_clean" expanded="False" title="Graph cleaning options" help="These options control the removal of small leftover sequences after bridging is complete.">
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234 <param argument="--min_component_size" optional="True" type="integer" value="" label="Unbridged graph components smaller than this size will be removed from the final graph" help="default = 1000"/>
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235 <param argument="--min_dead_end_size" optional="True" type="integer" value="" label="Graph dead ends smaller than this size will be removed from the final graph" help="default = 1000"/>
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236 </section>
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237
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238 <section name="lr_align" expanded="False" title="Long read alignment parameters" help="These options control the alignment of long reads to the assembly graph.">
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239 <param name="contamination_fasta" argument="--contamination" optional="True" type="data" format="fasta" label="FASTA file of known contamination in long reads, e.g. lambda, phiXm or puc18 spike-ins." />
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240 <param argument="--scores" optional="True" type="text" value="" label="Comma-delimited string of alignment scores: match, mismatch, gap open, gap extend" help="default = 3,-6,-5,-2"/>
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241 <param argument="--low_score" optional="True" type="integer" value="" label="Score threshold - alignments below this are considered poor" help="default = set automatically"/>
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242 </section>
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243 </inputs>
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244
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245 <outputs>
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246 <data format="txt" name="assembly_grapth" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
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247 <data format="fasta" name="assembly" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
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248 </outputs>
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249
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250 <tests>
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251 <test>
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252 <param name="fastq_input_selector" value="paired" />
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253 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
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254 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
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255 <param name="mode" value="normal" />
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256 <param name="no_correct" value="true" />
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257 <param name="no_rotate" value="false" />
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258 <param name="no_pilon" value="false" />
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259 <output ftype="fasta" name="assembly">
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260 <assert_contents>
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261 <has_text text="length=5386" />
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262 </assert_contents>
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263 </output>
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264 </test>
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265 <!--
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266 Following test corresponds to the command:
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267
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268 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \
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269 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \
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270 - -mode 'normal' - -no_correct
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271
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272 This command causes a segfault with the current version of unicycler on bioconda for Linux
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273 during the minimap step (which seems to be compiled C code). A gist of the log can be found
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274 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb.
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275 -->
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276 <test>
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277 <param name="fastq_input_selector" value="paired" />
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278 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
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279 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
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280 <param name="long_reads" value="onp.fa" ftype="fasta" />
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281 <param name="mode" value="normal" />
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282 <param name="no_correct" value="true" />
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283 <param name="no_rotate" value="false" />
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284 <param name="no_pilon" value="false" />
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285 <output ftype="fasta" name="assembly">
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286 <assert_contents>
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287 <has_text text="length=5386" />
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288 </assert_contents>
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289 </output>
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290 </test>
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291 </tests>
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292 <help><![CDATA[
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293
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294 **Unicycler**
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295
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296 Unicycler is a hybrid assembly pipeline for bacterial genomes. It uses both Illumina reads and long reads (PacBio or Nanopore) to produce complete and accurate assemblies. It is written by `Ryan Wick`_ at the University of Melbourne's Centre for Systems Genomics. Much of the description below is lifted from Unicycler's `github page`_.
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297
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298 .. _`Ryan Wick`: https://github.com/rrwick
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299 .. _`github page`: https://github.com/rrwick/Unicycler
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300
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301 -----
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302
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303 **Input data**
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304
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305 Unicycler accepts inputs short (Illumina) reads in FASTQ format. Galaxy places additional requirement of having these in FASTQ format with `Sanger encoding`_ of quality scores. Long reads (from Oxford Nanopore or PacBio) can be either in FASTQ of FASTA form.
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306
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307 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality
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308
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309 The input options are::
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310
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311 -1 SHORT1, --short1 SHORT1
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312 FASTQ file of short reads (first reads in each pair)
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313 -2 SHORT2, --short2 SHORT2
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314 FASTQ file of short reads (second reads in each pair)
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315 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED
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316 FASTQ file of unpaired short reads
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317 -l LONG, --long LONG
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318 FASTQ or FASTA file of long reads, if all reads are available at start.
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319
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320 -----
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321
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322 **Bridging mode**
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323
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324 Unicycler can be run in three modes: conservative, normal (the default) and bold, set with the --mode option. Conservative mode is least likely to produce a complete assembly but has a very low risk of misassembly. Bold mode is most likely to produce a complete assembly but carries greater risk of misassembly. Normal mode is intermediate regarding both completeness and misassembly risk. See `description of modes`_ for more information.
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325
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326 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold
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327
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328 The available modes are::
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329
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330 --mode {conservative,normal,bold}
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331 Bridging mode (default: normal)
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332 conservative = smaller contigs, lowest misassembly rate
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333 normal = moderate contig size and misassembly rate
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334 bold = longest contigs, higher misassembly rate
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335
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336 ----
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337
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338 **Skip SPAdes error correction step**
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339
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340 Sequencing data contains a substantial number of sequencing errors that manifest themselves as deviations (bulges and non-connected components) within the assembly graph. One of the ways to improve the graph even constructing it is to minimize the amount sequencing errors by performing error correction. SPAdes, which is used by Unicycler for error correction and assembly, uses `BayesHammer`_ to correct the reads. Here is a brief summary of what it does:
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341
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342 1. SPAdes (or rather BayesHammer) counts *k*-mers in reads and computed *k*-mer statistics that takes into account base quality values.
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343 2. `Hamming graph`_ is constructed for *k*-mers is which *k*-mers are nodes. In this graph edges connect nodes (*k*-mers) is they differ from each other by a number of nucleotides up to a certain threshold (the `Hamming distance`_). The graph is central to the error correction algorithm.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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344 3. At this step Bayesian subclustering of the graph produced in the previous step. For each *k*-mer we now know the center of its subcluster.
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345 4. Solid *k*-mers are derived from cluster centers and are assumed to be *error free*.
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346 5. Solid *k*-mers are mapped back to the reads and used to correct them.
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347
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348 This step takes considerable time, so if one need to quickly evaluate assemblies this step can be skipped. However, this is not recommended if one if trying to produce a final high quality assembly.
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349
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350 .. _`BayesHammer`: https://goo.gl/1iGkMe
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351 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph
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352 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance
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353
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354 This following option turns error correction on and off::
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355
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356 --no_correct
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357 Skip SPAdes error correction step
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358 (default: conduct SPAdes error correction)
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359
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360 -----
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361
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362 **Do not rotate completed replicons to start at a standard gene**
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363
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364 Unicycler uses TBLASTN to search for dnaA or repA alleles in each completed replicon. If one is found, the sequence is rotated and/or flipped so that it begins with that gene encoded on the forward strand. This provides consistently oriented assemblies and reduces the risk that a gene will be split across the start and end of the sequence.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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365
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366 The following option turns rotation on and off::
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367
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368 --no_rotate
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369 Do not rotate completed replicons
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370 to start at a standard gene
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371 (default: completed replicons are rotated)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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372
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373 **Do not use Pilon to polish the final assembly**
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374
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375 `Pilon`_ is a tool for improving overall quality of draft assemblies and finding variation among strains. Unicycler uses it for assembly *polishing*.
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376
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377 The following option turns pilon part of Unicycler pipeline on and off::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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378
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379 --no_pilon
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380 Do not use Pilon to polish the
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381 final assembly (default: Pilon is used)
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382
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383 .. _`Pilon`: https://github.com/broadinstitute/pilon/wiki
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384
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385 ------
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386
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387 **Expected number of linear sequences**
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388
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389 If you expect your sample to contain linear (non circular) sequences, set this option::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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390
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391 --expected_linear_seqs EXPECTED_LINEAR_SEQS
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392 The expected number of linear (i.e. non-circular)
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393 sequences in the underlying sequence
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394
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395 ----
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396
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397 **SPAdes options**
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398
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399 This section provides control of SPAdes options::
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400
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401 --min_kmer_frac MIN_KMER_FRAC
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402 Lowest k-mer size for SPAdes assembly,
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403 expressed as a fraction of the read length
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404 (default: 0.2)
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405 --max_kmer_frac MAX_KMER_FRAC
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406 Highest k-mer size for SPAdes assembly,
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407 expressed as a fraction of the read length
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408 (default: 0.95)
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409 --kmer_count KMER_COUNT
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410 Number of k-mer steps to use in
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411 SPAdes assembly (default: 10)
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412
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413 ----
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414
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415 **Rotation options**
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416
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417 Unicycler attempts to rotate circular assemblies to make sure that they begin at a consistent starting gene. The following parameters control assembly rotation::
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418
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419 --start_genes START_GENES
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420 FASTA file of genes for start point
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421 of rotated replicons
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422 (default: start_genes.fasta)
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423 --start_gene_id START_GENE_ID
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424 The minimum required BLAST percent identity
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425 for a start gene search
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426 (default: 90.0)
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427 --start_gene_cov START_GENE_COV
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428 The minimum required BLAST percent coverage
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
429 for a start gene search
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
430 (default: 95.0)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
431
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
432 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
433
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
434 **Graph cleaning options**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
435
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
436 These options control the removal of small leftover sequences after bridging is complete::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
437
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
438 --min_component_size MIN_COMPONENT_SIZE
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
439 Unbridged graph components smaller
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
440 than this size (bp) will be removed
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
441 from the final graph (default: 1000)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
442 --min_dead_end_size MIN_DEAD_END_SIZE
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
443 Graph dead ends smaller than this size (bp)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
444 will be removed from the final graph
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
445 (default: 1000)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
446
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
447 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
448
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
449 **Long read alignment options**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
450
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
451 These options control the alignment of long reads to the assembly graph::
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
452
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
453 --contamination CONTAMINATION
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
454 FASTA file of known contamination in long reads
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
455 --scores SCORES
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
456 Comma-delimited string of alignment scores:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
457 match, mismatch, gap open, gap extend
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
458 (default: 3,-6,-5,-2)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
459 --low_score LOW_SCORE
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
460 Score threshold - alignments below this
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
461 are considered poor
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
462 (default: set threshold automatically)
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
463
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
464 -----
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
465
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
466 **Outputs**
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
467
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
468 Galaxy's wrapped for Unicycler produces two outputs:
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
469
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
470 * final assembly in FASTA format
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
471 * final assembly grapth in graph format
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
472
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
473 While most will likely be interested in the FASTA dataset, the graph dataset is also quite useful and can be visualized using tools such as `Bandage`_.
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
474
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
475
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
476 .. _`Bandage`: https://github.com/rrwick/Bandage
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
477
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
478
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
479 ]]></help>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
480 <citations>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
481 <citation type="doi">10.1101/096412</citation>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
482 </citations>
15a21071f0a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
483 </tool>