Mercurial > repos > bgruening > flye
comparison flye.xml @ 4:3ee0ef312022 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 1143ac8397d6fefb3f18d33bb752ee3f13c072d6"
author | bgruening |
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date | Wed, 05 Feb 2020 19:37:18 -0500 |
parents | 1ce9b1d72ec3 |
children | de24438c9988 |
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3:1ce9b1d72ec3 | 4:3ee0ef312022 |
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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 |