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comparison flye.xml @ 6:d87d93f44f9e draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit d2767c87b1cc7459fd0d51c5c87f8e51d88d7f48"
author bgruening
date Thu, 14 Jan 2021 11:18:54 +0000
parents d43834703ab7
children 28898f6f2352
comparison
equal deleted inserted replaced
5:d43834703ab7 6:d87d93f44f9e
1 <tool id="flye" name="Flye assembly" version="2.6+galaxy0"> 1 <tool id="flye" name="Flye assembly" version="2.8.2+galaxy0">
2 <description>of long and error-prone reads</description> 2 <description>of long and error-prone reads</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
27 #for $counter, $input in enumerate($inputs): 27 #for $counter, $input in enumerate($inputs):
28 ./input_${counter}.$ext 28 ./input_${counter}.$ext
29 #end for 29 #end for
30 30
31 -o out_dir 31 -o out_dir
32 -g '$g'
33 -t \${GALAXY_SLOTS:-4} 32 -t \${GALAXY_SLOTS:-4}
34 -i $i 33 -i $i
35 #if $m: 34 #if $m:
36 -m '$m' 35 -m '$m'
37 #end if 36 #end if
38 #if $asm: 37 #if str($asm.asm_select) == "true":
39 --asm-coverage '$asm' 38 --asm-coverage '$asm.asm'
39 -g '$asm.g'
40 #end if 40 #end if
41 ${plasmids} 41 ${plasmids}
42 ${meta} 42 ${meta}
43 ${no_trestle} 43 ${no_trestle}
44 2>&1 44 2>&1
50 <option value="--nano-corr">Nanopore corrected</option> 50 <option value="--nano-corr">Nanopore corrected</option>
51 <option value="--pacbio-raw">PacBio raw</option> 51 <option value="--pacbio-raw">PacBio raw</option>
52 <option value="--pacbio-corr">PacBio corrected</option> 52 <option value="--pacbio-corr">PacBio corrected</option>
53 <option value="--subassemblies">high-quality contig-like input</option> 53 <option value="--subassemblies">high-quality contig-like input</option>
54 </param> 54 </param>
55 <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)">
56 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator>
57 </param>
58 <param argument="-i" type="integer" value="1" label="number of polishing iterations" /> 55 <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
59 <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" /> 56 <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
60 <param name="asm" argument="--asm-coverage" type="integer" optional="true" label="reduced coverage for initial disjointing assembly" /> 57
58 <conditional name="asm">
59 <param name="asm_select" type="select" label="description" help="">
60 <option value="true">Enable reduced coverage for initial disjointing assembly</option>
61 <option value="false" selected="true">Disable reduced coverage for initial disjointing assembly</option>
62 </param>
63 <when value="true">
64 <param name="asm" argument="--asm-coverage" type="integer" label="reduced coverage for initial disjointing assembly" />
65 <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)">
66 <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>
67 </param>
68 </when>
69 <when value="false" />
70 </conditional>
71
61 <param argument="--plasmids" type="boolean" truevalue="--plasmids" falsevalue="" checked="False" label="rescue short unassembled plasmids" /> 72 <param argument="--plasmids" type="boolean" truevalue="--plasmids" falsevalue="" checked="False" label="rescue short unassembled plasmids" />
62 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="perform metagenomic assembly" /> 73 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="perform metagenomic assembly" />
63 <param name="no_trestle" argument="--no-trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip trestle stage" /> 74 <param name="no_trestle" argument="--no-trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip trestle stage" />
64 </inputs> 75 </inputs>
65 <outputs> 76 <outputs>
71 </outputs> 82 </outputs>
72 <tests> 83 <tests>
73 <test> 84 <test>
74 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> 85 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
75 <param name="mode" value="--pacbio-raw"/> 86 <param name="mode" value="--pacbio-raw"/>
76 <param name="g" value="10000"/>
77 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/> 87 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
78 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> 88 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
79 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/> 89 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
80 <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/> 90 <output name="consensus" file="result1_assembly.fasta" ftype="fasta" compare="sim_size"/>
81 </test> 91 </test>
82 <test> 92 <test>
83 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> 93 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
84 <param name="mode" value="--nano-raw"/> 94 <param name="mode" value="--nano-raw"/>
85 <param name="g" value="10000"/>
86 <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/> 95 <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/>
87 <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> 96 <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
88 <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/> 97 <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
89 <output name="consensus" file="result2_assembly.fasta" ftype="fasta" compare="sim_size"/> 98 <output name="consensus" file="result2_assembly.fasta" ftype="fasta" compare="sim_size"/>
90 </test> 99 </test>
91 <test> 100 <test>
92 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> 101 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
93 <param name="mode" value="--nano-corr"/> 102 <param name="mode" value="--nano-corr"/>
94 <param name="g" value="10000"/>
95 <param name="i" value="2"/> 103 <param name="i" value="2"/>
96 <param name="asm" value="40"/> 104 <conditional name="asm">
105 <param name="asm_select" value="true" />
106 <param name="asm" value="40"/>
107 <param name="g" value="10000"/>
108 </conditional>
97 <output name="assembly_info" file="result3_assembly_info.txt" ftype="tabular" compare="sim_size"/> 109 <output name="assembly_info" file="result3_assembly_info.txt" ftype="tabular" compare="sim_size"/>
98 <output name="assembly_graph" file="result3_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> 110 <output name="assembly_graph" file="result3_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
99 <output name="assembly_gfa" file="result3_assembly_graph.gfa" ftype="txt" compare="sim_size"/> 111 <output name="assembly_gfa" file="result3_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
100 <output name="consensus" file="result3_assembly.fasta" ftype="fasta" compare="sim_size"/> 112 <output name="consensus" file="result3_assembly.fasta" ftype="fasta" compare="sim_size"/>
101 </test> 113 </test>
102 <test> 114 <test>
103 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> 115 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
104 <param name="mode" value="--pacbio-raw"/> 116 <param name="mode" value="--pacbio-raw"/>
105 <param name="g" value="10000"/>
106 <param name="i" value="1"/> 117 <param name="i" value="1"/>
107 <param name="meta" value="true"/> 118 <param name="meta" value="true"/>
108 <param name="plasmids" value="true"/> 119 <param name="plasmids" value="true"/>
109 <param name="no-trestle" value="true"/> 120 <param name="no-trestle" value="true"/>
110 <output name="assembly_info" file="result4_assembly_info.txt" ftype="tabular" compare="sim_size"/> 121 <output name="assembly_info" file="result4_assembly_info.txt" ftype="tabular" compare="sim_size"/>