Mercurial > repos > iuc > trycycler_consensus

annotate trycycler_consensus.xml @ 1:e59bee4565b3 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
author iuc
date Sat, 13 Feb 2021 17:29:47 +0000
parents 93c6a7423090
children 9ded6109434a
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e59bee4565b3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit e88166111fa3b6c57c870ea4cff6e012a1b1a912"
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1 <tool id='trycycler_consensus' name='Trycycler consensus' version='@TOOL_VERSION@' profile='20.01'>
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2 <description>generate a consensus contig sequence for each cluster</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro='edam_ontology' />
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7 <expand macro='requirements' />
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8 <version_command>trycycler --version</version_command>
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9 <command detect_errors='exit_code'><![CDATA[
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10 mkdir -p 'selected_cluster' &&
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11 ln -s '${cluster_all_seqs}' 'selected_cluster/2_all_seqs.fasta' &&
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12 ln -s '${reconcile_msa}' 'selected_cluster/3_msa.fasta' &&
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13 ln -s '${partition_reads}' 'selected_cluster/4_reads.fastq' &&
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14 trycycler consensus --cluster_dir 'selected_cluster'
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15 #if $linear
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16 --linear
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17 #end if
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18 --min_aligned_len $min_aligned_len
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19 --min_read_cov $min_read_cov
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20 --threads \${GALAXY_SLOTS:-2} &&
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21 mv 'selected_cluster/7_final_consensus.fasta' $consensus
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22 ]]> </command>
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23 <inputs>
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24 <param name='cluster_all_seqs' type='data' format='fasta' label='Reconciled cluster' help='Reconciled sequences file' />
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25 <param name='reconcile_msa' type='data' format='fasta' label='Reconcile msa' help='Multiple sequence alignment file' />
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26 <param name='partition_reads' type='data' format='fastq' label='Partition reads' help='Partitioned reads' />
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27 <param name='reads' type='data' format='fastq,fastq.gz' label='Long-read datasets' help='Long reads (FASTQ format) used to generate the assemblies' />
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28 <param argument='--linear' type='boolean' truevalue='--linear' falsevalue='' label='Input contigs are not circular' help='Use this option if your input contigs are not circular. It will disable the circularisation-correction steps in Trycycler reconcile.' />
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29 <param argument='--min_aligned_len' type='integer' min='500' max='3500' value='1000' label='Min bases aligned' help='Reads with less than this many bases aligned (default = 1000) will be ignored.' />
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30 <param argument='--min_read_cov' type='integer' min='0' max='100' value='90' label='Min read length covered by alignments' help='Reads with less than this percentage of their length covered by alignments (default = 90.0) will be ignored.' />
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31 </inputs>
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32 <outputs>
1
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33 <data name='consensus' format='fasta' label='${tool.name} on ${on_string}' />
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34 </outputs>
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35 <tests>
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36 <test>
1
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37 <param name='cluster_all_seqs' value='reconciled_cluster_01.fasta' />
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38 <param name='reconcile_msa' value='aligned_cluster_01.fasta' />
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39 <param name='partition_reads' value='partition_01.fastq' />
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40 <param name='reads' value='reads.fastq.gz' />
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41 <param name='min_aligned_len' value='1200' />
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42 <param name='min_read_cov' value='95' />
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43 <output name='consensus' file='consensus_sequence_01.fasta' />
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44 </test>
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45 <test>
1
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46 <param name='cluster_all_seqs' value='reconciled_cluster_02.fasta' />
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47 <param name='reconcile_msa' value='aligned_cluster_02.fasta' />
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48 <param name='partition_reads' value='partition_01.fastq' />
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49 <param name='reads' value='reads.fastq.gz' />
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50 <param name='min_aligned_len' value='1100' />
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51 <param name='min_read_cov' value='90' />
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52 <output name='consensus' file='consensus_sequence_02.fasta' />
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53 </test>
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54 <test>
1
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55 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
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56 <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
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57 <param name='partition_reads' value='partition_01.fastq' />
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58 <param name='reads' value='reads.fastq.gz' />
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59 <param name='min_aligned_len' value='1300' />
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60 <param name='min_read_cov' value='97' />
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61 <output name='consensus' file='consensus_sequence_03.fasta' />
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62 </test>
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63 <test>
1
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64 <param name='cluster_all_seqs' value='reconciled_cluster_03.fasta' />
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65 <param name='reconcile_msa' value='aligned_cluster_03.fasta' />
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66 <param name='partition_reads' value='partition_01.fastq' />
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67 <param name='reads' value='reads.fastq.gz' />
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68 <param name='min_aligned_len' value='1000' />
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69 <param name='min_read_cov' value='87' />
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70 <output name='consensus' file='consensus_sequence_04.fasta' />
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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75 .. class:: infomark
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76
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77 **Purpose**
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78
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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79 **Trycycler consensus** generate a consensus contig sequence for each cluster. It does this by converting the MSA into a graph form. When there is a tie between options, Trycycler aligns the reads to the alternative sequences and chooses the option with the best read alignment scores.
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80
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81 ::
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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82
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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83 GGAGGAGCTTTT-CGCCGCAGTCAACGAA-TAGCGTCTGAAAACGTGTATCAT
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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84 GGAGGAGCTTTTTCGCCGCAGTCAAC--A-TAGCGTCTGAAAACGTGTATCAT
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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85 GGAGGAGCTTTTTCGCCGCAGTCAAC--ATTAGCGTCTGAAAACGTGTATCAT
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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86 GGAGGAGCTTTTTCGCCGCAGTCAAC--A-TAGCGTCTGAAAACGTGTATCAT
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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87 GGAGGAGCTTTT-CGCCGCAGTCAAC--A-TAGCGTCTGAAAACGTGTATCAT
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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88
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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89 From the hypothetical MSA, Trycycler generates a variation graph:
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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90
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91 ::
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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92
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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93 ↗ - ↘ ↗ GAA- ↘
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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94 ↗ T ↘ ↗ --A- ↘
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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95 GGAGGAGCTTTT → T → CGCCGCAGTCAAC → --AT → TAGCGTCTGAAAACGTGTATCAT
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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96 ↘ T ↗ ↘ --A- ↗
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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97 ↘ - ↗ ↘ --A- ↗
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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98
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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99
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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100
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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101 The first thing Trycycler uses to choose variants is minimum total Hamming distance to the other variants. In cases of a minimum total Hamming distance tie, Trycycler will align the reads to each possibility and choose the option with the highest total read alignment score. Read alignment scores are calculated using a simple scheme: match score = 1, mismatch penalty = 1, gap open/extension penalty = 1. More information in the `documentation <https://github.com/rrwick/Trycycler/wiki/How-variants-are-chosen-for-the-consensus-sequence/>`_.
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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102
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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103
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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104
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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105 ----
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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106
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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107 .. class:: infomark
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108
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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109 **Input**
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110
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111 This tool requires the output generated by **Trycylcler reconcile**, **Trycycler msa** and **Trycycler partition**.
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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112
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113
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114 ----
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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115
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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116 .. class:: infomark
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117
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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118 **Output**
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119
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120 It generates a fasta file with the consesus sequence the cluster.
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121
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122
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123 ----
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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124
93c6a7423090 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trycycler commit 9d7c4277b0f96aacd466f2d497e08edcca3fa238"
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125 .. class:: infomark
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126
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127 @PIPELINE@
1
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128 ]]> </help>
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129 <expand macro='citations' />
0
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130 </tool>