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annotate flye.xml @ 4:3ee0ef312022 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
author bgruening
date Wed, 05 Feb 2020 19:37:18 -0500
parents 1ce9b1d72ec3
children de24438c9988
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3ee0ef312022 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
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1 <tool id="flye" name="Flye assembly" version="2.6">
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2 <description>of long and error-prone reads</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="requirements" />
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7 <version_command>flye --version</version_command>
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8 <command detect_errors="exit_code">
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9 <![CDATA[
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10
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11 #for $counter, $input in enumerate($inputs):
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12
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13 #if $input.is_of_type('fastqsanger', 'fastq'):
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14 #set $ext = 'fastq'
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15 #elif $input.is_of_type('fastqsanger.gz'):
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16 #set $ext = 'fastq.gz'
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17 #elif $input.is_of_type('fasta.gz'):
1
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18 #set $ext = 'fasta.gz'
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19 #elif $input.is_of_type('fasta'):
1
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20 #set $ext = 'fasta'
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21 #end if
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22 ln -s '$input' ./input_${counter}.${ext} &&
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23 #end for
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24
0
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25 flye
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26 $mode
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27 #for $counter, $input in enumerate($inputs):
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28 ./input_${counter}.$ext
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29 #end for
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30
3
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31 -o out_dir
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32 -g '$g'
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33 -t \${GALAXY_SLOTS:-4}
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34 -i $i
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35 #if $m:
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36 -m '$m'
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37 #end if
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38 #if $asm:
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39 --asm-coverage '$asm'
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40 #end if
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41 ${plasmids}
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42 ${meta}
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43 ${no_trestle}
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44 2>&1
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45 ]]></command>
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46 <inputs>
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47 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
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48 <param name="mode" type="select" label="Mode">
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49 <option value="--nano-raw">Nanopore raw</option>
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50 <option value="--nano-corr">Nanopore corrected</option>
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51 <option value="--pacbio-raw">PacBio raw</option>
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52 <option value="--pacbio-corr">PacBio corrected</option>
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53 <option value="--subassemblies">high-quality contig-like input</option>
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54 </param>
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55 <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)">
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56 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
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57 </param>
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58 <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
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59 <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
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60 <param name="asm" argument="--asm-coverage" type="integer" optional="true" label="reduced coverage for initial disjointing assembly" />
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61 <param argument="--plasmids" type="boolean" truevalue="--plasmids" falsevalue="" checked="False" label="rescue short unassembled plasmids" />
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62 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="perform metagenomic assembly" />
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63 <param name="no_trestle" argument="--no-trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip trestle stage" />
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64 </inputs>
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65 <outputs>
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66 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string} (consensus)"/>
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67 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string} (assembly_graph)"/>
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68 <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)"/>
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69 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
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70 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/>
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71 </outputs>
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72 <tests>
3
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73 <test>
2
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74 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
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75 <param name="mode" value="--pacbio-raw"/>
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76 <param name="g" value="10000"/>
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77 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
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78 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
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79 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
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80 <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/>
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81 </test>
3
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82 <test>
2
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83 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
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84 <param name="mode" value="--nano-raw"/>
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85 <param name="g" value="10000"/>
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86 <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/>
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87 <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
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88 <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
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89 <output name="consensus" file="result2_assembly.fasta" ftype="fasta" compare="sim_size"/>
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90 </test>
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91 <test>
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92 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
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93 <param name="mode" value="--nano-corr"/>
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94 <param name="g" value="10000"/>
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95 <param name="i" value="2"/>
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96 <param name="asm" value="40"/>
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97 <output name="assembly_info" file="result3_assembly_info.txt" ftype="tabular" compare="sim_size"/>
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98 <output name="assembly_graph" file="result3_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
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99 <output name="assembly_gfa" file="result3_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
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100 <output name="consensus" file="result3_assembly.fasta" ftype="fasta" compare="sim_size"/>
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101 </test>
3
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102 <test>
2
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103 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
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104 <param name="mode" value="--pacbio-raw"/>
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105 <param name="g" value="10000"/>
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106 <param name="i" value="1"/>
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107 <param name="meta" value="true"/>
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108 <param name="plasmids" value="true"/>
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109 <param name="no-trestle" value="true"/>
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110 <output name="assembly_info" file="result4_assembly_info.txt" ftype="tabular" compare="sim_size"/>
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111 <output name="assembly_graph" file="result4_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
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112 <output name="assembly_gfa" file="result4_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
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113 <output name="consensus" file="result4_assembly.fasta" ftype="fasta" compare="sim_size"/>
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114 </test>
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115 </tests>
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116 <help><![CDATA[
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117
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118 Input reads could be in FASTA or FASTQ format, uncompressed
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119 or compressed with gz. Currenlty, raw and corrected reads
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120 from PacBio and ONT are supported. The expected error rates are
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121 <30% for raw and <2% for corrected reads. Additionally,
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122 --subassemblies option performs a consensus assembly of multiple
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123 sets of high-quality contigs. You may specify multiple
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124 files with reads (separated by spaces). Mixing different read
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125 types is not yet supported.
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126
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127 You must provide an estimate of the genome size as input,
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128 which is used for solid k-mers selection. The estimate could
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129 be rough (e.g. withing 0.5x-2x range) and does not affect
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130 the other assembly stages. Standard size modificators are
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131 supported (e.g. 5m or 2.6g).
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132
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133 ]]></help>
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134 <expand macro="citations" />
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135 </tool>