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comparison flye.xml @ 4:fed3d7b3ef6b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
author bgruening
date Thu, 06 Feb 2020 00:36:53 +0000
parents c5417aa9eb4f
children d43834703ab7
comparison
equal deleted inserted replaced
3:c5417aa9eb4f 4:fed3d7b3ef6b
1 <tool id="flye" name="Assembly" version="2.3.7"> 1 <tool id="flye" name="Flye assembly" version="2.6">
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" />
33 -t \${GALAXY_SLOTS:-4} 33 -t \${GALAXY_SLOTS:-4}
34 -i $i 34 -i $i
35 #if $m: 35 #if $m:
36 -m '$m' 36 -m '$m'
37 #end if 37 #end if
38 #if $asm:
39 --asm-coverage '$asm'
40 #end if
41 ${plasmids}
42 ${meta}
43 ${no_trestle}
38 2>&1 44 2>&1
39 ]]></command> 45 ]]></command>
40 <inputs> 46 <inputs>
41 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" /> 47 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz,fastqsanger.gz,fastqsanger" multiple="true" label="Input reads" />
42 <param name="mode" type="select" label="Mode"> 48 <param name="mode" type="select" label="Mode">
49 <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)"> 55 <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)">
50 <validator type="regex" message="Genome size must be a float or integer, optionally followed by the a unit prefix (kmg)">^([0-9]*[.])?[0-9]+[kmg]?$</validator> 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]?$</validator>
51 </param> 57 </param>
52 <param argument="-i" type="integer" value="1" label="number of polishing iterations" /> 58 <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
53 <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" /> 59 <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
60 <param name="asm" argument="--asm-coverage" type="integer" optional="true" label="reduced coverage for initial disjointing assembly" />
61 <param argument="--plasmids" type="boolean" truevalue="--plasmids" falsevalue="" checked="False" label="rescue short unassembled plasmids" />
62 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="False" label="perform metagenomic assembly" />
63 <param name="no_trestle" argument="--no-trestle" type="boolean" truevalue="--no-trestle" falsevalue="" checked="False" label="skip trestle stage" />
54 </inputs> 64 </inputs>
55 <outputs> 65 <outputs>
56 <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/> 66 <data name="consensus" format="fasta" from_work_dir="out_dir/assembly.fasta" label="${tool.name} on ${on_string} (consensus)"/>
57 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
58 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string} (assembly_graph)"/> 67 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.gv" label="${tool.name} on ${on_string} (assembly_graph)"/>
59 <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)"/> 68 <data name="assembly_gfa" format="txt" from_work_dir="out_dir/assembly_graph.gfa" label="${tool.name} on ${on_string} (Graphical Fragment Assembly)"/>
69 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
60 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/> 70 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/>
61 </outputs> 71 </outputs>
62 <tests> 72 <tests>
63 <test> 73 <test>
64 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> 74 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
65 <param name="mode" value="--pacbio-raw"/> 75 <param name="mode" value="--pacbio-raw"/>
66 <param name="g" value="10000"/> 76 <param name="g" value="10000"/>
67 <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
68 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/> 77 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular" compare="sim_size"/>
69 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> 78 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
70 <output name="assembly_gfa" file="result1_assembly_graph.gfa" ftype="txt" compare="sim_size"/> 79 <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"/>
71 </test> 81 </test>
72 <test> 82 <test>
73 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> 83 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
74 <param name="mode" value="--nano-raw"/> 84 <param name="mode" value="--nano-raw"/>
75 <param name="g" value="10000"/> 85 <param name="g" value="10000"/>
76 <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta" compare="sim_size"/>
77 <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/> 86 <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular" compare="sim_size"/>
78 <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/> 87 <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
79 <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/> 88 <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"/>
90 </test>
91 <test>
92 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
93 <param name="mode" value="--nano-corr"/>
94 <param name="g" value="10000"/>
95 <param name="i" value="2"/>
96 <param name="asm" value="40"/>
97 <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"/>
99 <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"/>
80 </test> 101 </test>
81 <test> 102 <test>
82 <param name="inputs" ftype="fasta" value="nanopore.fasta"/> 103 <param name="inputs" ftype="fasta" value="nanopore.fasta"/>
83 <param name="mode" value="--pacbio-raw"/> 104 <param name="mode" value="--pacbio-raw"/>
84 <param name="g" value="10000"/> 105 <param name="g" value="10000"/>
85 <param name="i" value="2"/> 106 <param name="i" value="1"/>
86 <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta" compare="sim_size"/> 107 <param name="meta" value="true"/>
87 <output name="assembly_gfa" file="result2_assembly_graph.gfa" ftype="txt" compare="sim_size"/> 108 <param name="plasmids" value="true"/>
109 <param name="no-trestle" value="true"/>
110 <output name="assembly_info" file="result4_assembly_info.txt" ftype="tabular" compare="sim_size"/>
111 <output name="assembly_graph" file="result4_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
112 <output name="assembly_gfa" file="result4_assembly_graph.gfa" ftype="txt" compare="sim_size"/>
113 <output name="consensus" file="result4_assembly.fasta" ftype="fasta" compare="sim_size"/>
88 </test> 114 </test>
89 </tests> 115 </tests>
90 <help><![CDATA[ 116 <help><![CDATA[
91 117
92 Input reads could be in FASTA or FASTQ format, uncompressed 118 Input reads could be in FASTA or FASTQ format, uncompressed