annotate unicycler.xml @ 1:f13d0498a199 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f08410ac745c478d6948079f571a5f306d27854
author iuc
date Fri, 29 Sep 2017 11:03:48 -0400
parents e9c1cdb9f9dc
children e92675014ac9
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f13d0498a199 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f08410ac745c478d6948079f571a5f306d27854
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1 <tool id="unicycler" name="Create assemblies with Unicycler" version="0.4.1">
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e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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2 <requirements>
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f13d0498a199 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 1f08410ac745c478d6948079f571a5f306d27854
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3 <requirement type="package" version="0.4.1">unicycler</requirement>
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4 </requirements>
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5 <command detect_errors="exit_code"><![CDATA[
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7 ## Preparing files
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9 #if str( $paired_unpaired.fastq_input_selector ) == "paired":
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e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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11 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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12 ln -s '${paired_unpaired.fastq_input1}' fq1.fastq &&
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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13 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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14 ln -s '${paired_unpaired.fastq_input1}' fq1.fastq.gz &&
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15 #end if
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e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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17 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger'):
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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18 ln -s '${paired_unpaired.fastq_input2}' fq2.fastq &&
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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19 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz'):
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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20 ln -s '${paired_unpaired.fastq_input1}' fq2.fastq.gz &&
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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21 #end if
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e9c1cdb9f9dc 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":
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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25 #if $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger'):
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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26 ln -s '${paired_unpaired.fastq_input1.forward}' fq1.fastq &&
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27 #elif $paired_unpaired.fastq_input1.forward.is_of_type('fastqsanger.gz'):
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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28 ln -s '${paired_unpaired.fastq_input1.forward}' fq1.fastq.gz &&
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29 #end if
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e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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31 #if $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger'):
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32 ln -s '${paired_unpaired.fastq_input1.reverse}' fq2.fastq &&
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33 #elif $paired_unpaired.fastq_input1.reverse.is_of_type('fastqsanger.gz'):
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34 ln -s '${paired_unpaired.fastq_input2.reverse}' fq2.fastq.gz &&
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35 #end if
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e9c1cdb9f9dc 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":
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38
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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39 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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40 ln -s '${paired_unpaired.fastq_input1}' fq.fastq &&
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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41 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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42 ln -s '${paired_unpaired.fastq_input1}' fq.fastq.gz &&
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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43 #end if
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44
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45 #end if
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46
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47 ## Get location for pilon installation
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48
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49 pilon=`pilon --jar_dir` &&
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50
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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51 #if $long_reads:
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52 #if $long_reads.is_of_type('fastqsanger'):
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53 #set lr = "lr.fastq"
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54 ln -s '${long_reads}' lr.fastq &&
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55 #elif $long_reads.is_of_type('fastqsanger.gz'):
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56 #set lr = "lr.fastq.gz"
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57 ln -s '${long_reads}' lr.fastq.gz &&
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58 #elif $long_reads.is_of_type('fasta'):
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59 #set lr = "lr.fasta"
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60 ln -s '${long_reads}' lr.fasta &&
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61 #end if
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62 #end if
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63
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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64 ## Running Unicycler
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65
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66 unicycler -t "\${GALAXY_SLOTS:-4}"
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67
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68 -o ./
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69 --verbosity 3
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70 --pilon_path \$pilon
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71
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72 #if str( $paired_unpaired.fastq_input_selector ) != "single":
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73
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74 #if $paired_unpaired.fastq_input1.is_of_type('fastqsanger'):
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75 -1 fq1.fastq
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76 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
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77 -1 fq1.fastq.gz
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78 #end if
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79
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80 #if $paired_unpaired.fastq_input2.is_of_type('fastqsanger'):
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81 -2 fq2.fastq
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82 #elif $paired_unpaired.fastq_input2.is_of_type('fastqsanger.gz'):
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83 -2 fq2.fastq.gz
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
84 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
85
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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86 #else:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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87
e9c1cdb9f9dc 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'):
e9c1cdb9f9dc 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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
90 #elif $paired_unpaired.fastq_input1.is_of_type('fastqsanger.gz'):
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
91 -s fq.fastq.gz
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
92 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
93
e9c1cdb9f9dc 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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
95
e9c1cdb9f9dc 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:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
97
e9c1cdb9f9dc 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 $lr
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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99
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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100 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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101
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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102 ## General Unicycler Options section
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
103 ## ----------------------------------------------------------
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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104
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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105 --mode '${uc_opt.mode}'
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
106
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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107 #if $uc_opt.min_fasta_length:
e9c1cdb9f9dc 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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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109 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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110
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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111 #if $uc_opt.lin_seq:
e9c1cdb9f9dc 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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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113 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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114
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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115 $uc_opt.no_correct
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
116 $uc_opt.no_rotate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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117
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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118 ## Rotation Options section
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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119 ## ----------------------------------------------------------
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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120
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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121 #if $spades.min_kmer_frac:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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122 --min_kmer_frac $spades.min_kmer_frac
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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123 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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124
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
125 #if $spades.max_kmer_frac:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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126 --max_kmer_frac $spades.max_kmer_frac
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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127 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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128
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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129 #if $spades.kmer_count:
e9c1cdb9f9dc 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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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131 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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132
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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133 ## Rotation Options section
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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134 ## ----------------------------------------------------------
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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135
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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136 #if $rotation.start_genes:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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137 --start_genes '${rotation.rotation_fasta.start_genes}'
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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138 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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139
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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140 #if $rotation.start_gene_id:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
141 --start_gene_id $rotation.start_gene_id
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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142 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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143
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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144 #if $rotation.start_gene_cov:
e9c1cdb9f9dc 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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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146 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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147
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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148 ## Pilon Options section
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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149 ## ----------------------------------------------------------
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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150
e9c1cdb9f9dc 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:
e9c1cdb9f9dc 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
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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153 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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154
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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155 ## Graph Cleaning Options sdection
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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156 ## ----------------------------------------------------------
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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157
e9c1cdb9f9dc 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:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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159 --min_component_size $graph_clean.min_component_size
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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160 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
161 #if $graph_clean.min_dead_end_size:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
162 --min_dead_end_size $graph_clean.min_dead_end_size
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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163 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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164
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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165 ## Long Read Alignment Options
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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diff changeset
166 ## ----------------------------------------------------------
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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167
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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168
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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169 #if $lr_align.contamination_fasta:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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170 --contamination '${lr_align.contamination_fasta}'
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171 #end if
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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172
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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173 #if $lr_align.scores:
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174 --scores '${lr_align.scores}'
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175 #end if
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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
1
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181 ## Miniasm requires racon, which is not available for python 3.x
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182 --no_miniasm
0
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183
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184 ]]></command>
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185
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186 <inputs>
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187 <conditional name="paired_unpaired">
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188 <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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189 <option selected="True" value="paired">Paired</option>
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190 <option value="paired_collection">Paired Collection</option>
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191 <option value="single">Single</option>
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192 </param>
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193 <when value="paired">
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194 <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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195 <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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196 </when>
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197 <when value="paired_collection">
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198 <param name="fastq_input1" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" />
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199 </when>
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200 <when value="single">
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201 <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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202 </when>
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203 </conditional>
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204 <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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205
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206 <section name="uc_opt" expanded="True" title="Unicycler options">
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207 <param argument="--mode" type="select" label="Select Bridging mode">
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208 <option value="conservative">Conservative (smaller contigs, lower misassembly)</option>
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209 <option value="normal" selected="True">Normal (moderate contig size and misassembly rate)</option>
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210 <option value="bold">Bold (longest contigs, higher misassembly rate)</option>
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211 </param>
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212 <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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213 <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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214 <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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215 <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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216 <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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217 </section>
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218
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219 <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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220 <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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221 <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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222 <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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223 </section>
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224
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225 <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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226 <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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227 <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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228 <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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229 </section>
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230
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231 <section name="pilon" title="Pilon options" expanded="False">
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232 <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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233 </section>
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234
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235 <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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236 <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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237 <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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238 </section>
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239
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240 <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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241 <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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242 <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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243 <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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244 </section>
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245 </inputs>
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246
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247 <outputs>
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248 <data format="txt" name="assembly_grapth" from_work_dir="assembly.gfa" label="${tool.name} on ${on_string}: Final Assembly Graph" />
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249 <data format="fasta" name="assembly" from_work_dir="assembly.fasta" label="${tool.name} on ${on_string}: Final Assembly"/>
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250 </outputs>
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251
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252 <tests>
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253 <test>
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254 <param name="fastq_input_selector" value="paired" />
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255 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
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256 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
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257 <param name="mode" value="normal" />
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258 <param name="no_correct" value="true" />
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259 <param name="no_rotate" value="false" />
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260 <param name="no_pilon" value="false" />
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261 <output ftype="fasta" name="assembly">
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262 <assert_contents>
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263 <has_text text="length=5386" />
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264 </assert_contents>
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265 </output>
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266 </test>
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267 <!--
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268 Following test corresponds to the command:
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269
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270 unicycler -t "${GALAXY_SLOTS:-8}" -o ./ - -verbose 3 - -pilon_path `pilon - -jar_dir` \
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271 -1 test-data/phix_f.fq.gz -2 test-data/phix_r.fq.gz -l test-data/onp.fa \
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272 - -mode 'normal' - -no_correct
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273
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274 This command causes a segfault with the current version of unicycler on bioconda for Linux
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275 during the minimap step (which seems to be compiled C code). A gist of the log can be found
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276 at: https://gist.github.com/jmchilton/b411b695170c1daea6589f5d76e326cb.
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277 -->
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278 <test>
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279 <param name="fastq_input_selector" value="paired" />
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280 <param name="fastq_input1" value="phix_f.fq.gz" ftype="fastqsanger" />
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281 <param name="fastq_input2" value="phix_r.fq.gz" ftype="fastqsanger" />
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282 <param name="long_reads" value="onp.fa" ftype="fasta" />
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283 <param name="mode" value="normal" />
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284 <param name="no_correct" value="true" />
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285 <param name="no_rotate" value="false" />
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286 <param name="no_pilon" value="false" />
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287 <output ftype="fasta" name="assembly">
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288 <assert_contents>
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289 <has_text text="length=5386" />
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290 </assert_contents>
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291 </output>
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292 </test>
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293 </tests>
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294 <help><![CDATA[
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295
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296 **Unicycler**
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297
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298 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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299
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300 .. _`Ryan Wick`: https://github.com/rrwick
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301 .. _`github page`: https://github.com/rrwick/Unicycler
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302
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303 -----
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304
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305 **Input data**
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306
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307 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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308
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309 .. _`Sanger encoding`: https://en.wikipedia.org/wiki/FASTQ_format#Quality
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310
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311 The input options are::
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312
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313 -1 SHORT1, --short1 SHORT1
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314 FASTQ file of short reads (first reads in each pair)
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315 -2 SHORT2, --short2 SHORT2
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316 FASTQ file of short reads (second reads in each pair)
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317 -s SHORT_UNPAIRED, --short_unpaired SHORT_UNPAIRED
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318 FASTQ file of unpaired short reads
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319 -l LONG, --long LONG
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320 FASTQ or FASTA file of long reads, if all reads are available at start.
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321
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322 -----
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323
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324 **Bridging mode**
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325
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326 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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327
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328 .. _`description of modes`: https://github.com/rrwick/Unicycler#conservative-normal-and-bold
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329
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330 The available modes are::
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331
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332 --mode {conservative,normal,bold}
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333 Bridging mode (default: normal)
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334 conservative = smaller contigs, lowest misassembly rate
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335 normal = moderate contig size and misassembly rate
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336 bold = longest contigs, higher misassembly rate
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337
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338 ----
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339
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340 **Skip SPAdes error correction step**
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341
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342 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:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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343
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344 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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345 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.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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346 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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347 4. Solid *k*-mers are derived from cluster centers and are assumed to be *error free*.
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348 5. Solid *k*-mers are mapped back to the reads and used to correct them.
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349
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350 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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351
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352 .. _`BayesHammer`: https://goo.gl/1iGkMe
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353 .. _`Hamming graph`: https://en.wikipedia.org/wiki/Hamming_graph
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354 .. _`Hamming distance`: https://en.wikipedia.org/wiki/Hamming_distance
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355
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356 This following option turns error correction on and off::
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357
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358 --no_correct
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359 Skip SPAdes error correction step
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360 (default: conduct SPAdes error correction)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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361
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362 -----
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363
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364 **Do not rotate completed replicons to start at a standard gene**
e9c1cdb9f9dc 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 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.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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367
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368 The following option turns rotation on and off::
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369
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370 --no_rotate
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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371 Do not rotate completed replicons
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372 to start at a standard gene
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373 (default: completed replicons are rotated)
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374
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375 **Do not use Pilon to polish the final assembly**
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376
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377 `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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378
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379 The following option turns pilon part of Unicycler pipeline on and off::
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380
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381 --no_pilon
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382 Do not use Pilon to polish the
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383 final assembly (default: Pilon is used)
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384
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385 .. _`Pilon`: https://github.com/broadinstitute/pilon/wiki
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386
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387 ------
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388
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389 **Expected number of linear sequences**
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390
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391 If you expect your sample to contain linear (non circular) sequences, set this option::
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392
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393 --expected_linear_seqs EXPECTED_LINEAR_SEQS
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394 The expected number of linear (i.e. non-circular)
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395 sequences in the underlying sequence
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396
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397 ----
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398
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399 **SPAdes options**
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400
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401 This section provides control of SPAdes options::
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402
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403 --min_kmer_frac MIN_KMER_FRAC
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404 Lowest k-mer size for SPAdes assembly,
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405 expressed as a fraction of the read length
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406 (default: 0.2)
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407 --max_kmer_frac MAX_KMER_FRAC
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408 Highest k-mer size for SPAdes assembly,
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409 expressed as a fraction of the read length
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410 (default: 0.95)
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411 --kmer_count KMER_COUNT
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412 Number of k-mer steps to use in
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413 SPAdes assembly (default: 10)
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414
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415 ----
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416
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417 **Rotation options**
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418
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419 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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420
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
421 --start_genes START_GENES
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
422 FASTA file of genes for start point
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
423 of rotated replicons
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
424 (default: start_genes.fasta)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
425 --start_gene_id START_GENE_ID
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
426 The minimum required BLAST percent identity
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
427 for a start gene search
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
428 (default: 90.0)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
429 --start_gene_cov START_GENE_COV
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
430 The minimum required BLAST percent coverage
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
431 for a start gene search
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
432 (default: 95.0)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
433
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
434 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
435
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
436 **Graph cleaning options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
437
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
438 These options control the removal of small leftover sequences after bridging is complete::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
439
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
440 --min_component_size MIN_COMPONENT_SIZE
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
441 Unbridged graph components smaller
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
442 than this size (bp) will be removed
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
443 from the final graph (default: 1000)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
444 --min_dead_end_size MIN_DEAD_END_SIZE
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
445 Graph dead ends smaller than this size (bp)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
446 will be removed from the final graph
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
447 (default: 1000)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
448
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
449 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
450
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
451 **Long read alignment options**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
452
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
453 These options control the alignment of long reads to the assembly graph::
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
454
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
455 --contamination CONTAMINATION
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
456 FASTA file of known contamination in long reads
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
457 --scores SCORES
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
458 Comma-delimited string of alignment scores:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
459 match, mismatch, gap open, gap extend
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
460 (default: 3,-6,-5,-2)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
461 --low_score LOW_SCORE
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
462 Score threshold - alignments below this
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
463 are considered poor
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
464 (default: set threshold automatically)
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
465
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
466 -----
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
467
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
468 **Outputs**
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
469
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
470 Galaxy's wrapped for Unicycler produces two outputs:
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
471
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
472 * final assembly in FASTA format
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
473 * final assembly grapth in graph format
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
474
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
475 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`_.
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
476
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
477
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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478 .. _`Bandage`: https://github.com/rrwick/Bandage
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
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diff changeset
479
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
480
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
481 ]]></help>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
482 <citations>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
483 <citation type="doi">10.1101/096412</citation>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
iuc
parents:
diff changeset
484 </citations>
e9c1cdb9f9dc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/unicycler commit 97c19413f9d7e85c013b82ffafa73632c79c8f0b
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485 </tool>