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comparison flye.xml @ 0:d9f4c141d88a draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flye commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author bgruening
date Tue, 25 Sep 2018 05:24:27 -0400
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children cd256484eb1a
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-1:000000000000 0:d9f4c141d88a
1 <tool id="flye" name="Assembly" version="2.3.5">
2 <description>of long and error-prone reads</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <version_command>flye --version</version_command>
8 <command detect_errors="exit_code">
9 <![CDATA[
10
11 #for $counter, $input in enumerate($inputs):
12 ln -s '$input' ./input_${counter}.${input.ext} &&
13 #end for
14
15 flye
16 $mode
17 #for $counter, $input in enumerate($inputs):
18 ./input_${counter}.${input.ext}
19 #end for
20
21 -o out_dir
22 -g '$g'
23 -t \${GALAXY_SLOTS:-4}
24 -i $i
25 #if $m:
26 -m '$m'
27 #end if
28 2>&1
29 ]]></command>
30 <inputs>
31 <param name="inputs" type="data" format="fasta,fasta.gz,fastq,fastq.gz" multiple="true" label="Input reads" />
32 <param name="mode" type="select" label="Mode">
33 <option value="--nano-raw">Nanopore raw</option>
34 <option value="--nano-corr">Nanopore corrected</option>
35 <option value="--pacbio-raw">PacBio raw</option>
36 <option value="--pacbio-corr">PacBio corrected</option>
37 <option value="--subassemblies">high-quality contig-like input</option>
38 </param>
39 <param argument="-g" type="text" label="estimated genome size (for example, 5m or 2.6g)">
40 <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]?$</validator>
41 </param>
42 <param argument="-i" type="integer" value="1" label="number of polishing iterations" />
43 <param argument="-m" type="integer" optional="true" label="minimum overlap between reads (default: auto)" />
44 </inputs>
45 <outputs>
46 <data name="contigs" format="fasta" from_work_dir="out_dir/contigs.fasta" label="${tool.name} on ${on_string} (contigs)"/>
47 <data name="scaffolds" format="fasta" from_work_dir="out_dir/scaffolds.fasta" label="${tool.name} on ${on_string} (scaffolds)"/>
48 <data name="assembly_info" format="tabular" from_work_dir="out_dir/assembly_info.txt" label="${tool.name} on ${on_string} (assembly_info)"/>
49 <data name="assembly_graph" format="graph_dot" from_work_dir="out_dir/assembly_graph.dot" label="${tool.name} on ${on_string} (assembly_graph)"/>
50 <data name="flye_log" format="txt" from_work_dir="out_dir/flye.log" label="${tool.name} on ${on_string} (log)"/>
51 </outputs>
52 <tests>
53 <test>
54 <param name="inputs" ftype="fasta" value="E.coli_PacBio_40x_first_200_reads.fasta"/>
55 <param name="mode" value="--pacbio-raw"/>
56 <param name="g" value="1m"/>
57 <output name="contigs" file="result1_contigs.fasta" ftype="fasta"/>
58 <output name="scaffolds" file="result1_scaffolds.fasta" ftype="fasta"/>
59 <output name="assembly_info" file="result1_assembly_info.txt" ftype="tabular"/>
60 <output name="assembly_graph" file="result1_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
61 </test>
62 <test>
63 <param name="inputs" ftype="fasta" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
64 <param name="mode" value="--nano-raw"/>
65 <param name="g" value="100000"/>
66 <output name="contigs" file="result2_contigs.fasta" ftype="fasta"/>
67 <output name="scaffolds" file="result2_scaffolds.fasta" ftype="fasta"/>
68 <output name="assembly_info" file="result2_assembly_info.txt" ftype="tabular"/>
69 <output name="assembly_graph" file="result2_assembly_graph.dot" ftype="graph_dot" compare="sim_size"/>
70 </test>
71 <test>
72 <param name="inputs" ftype="fasta" value="E.coli_PacBio_40x_first_200_reads.fasta"/>
73 <param name="mode" value="--pacbio-raw"/>
74 <param name="g" value="1.1m"/>
75 <param name="i" value="2"/>
76 <output name="contigs" file="result3_contigs.fasta" ftype="fasta"/>
77 <output name="scaffolds" file="result3_scaffolds.fasta" ftype="fasta"/>
78 </test>
79 </tests>
80 <help><![CDATA[
81
82 Input reads could be in FASTA or FASTQ format, uncompressed
83 or compressed with gz. Currenlty, raw and corrected reads
84 from PacBio and ONT are supported. The expected error rates are
85 <30% for raw and <2% for corrected reads. Additionally,
86 --subassemblies option performs a consensus assembly of multiple
87 sets of high-quality contigs. You may specify multiple
88 files with reads (separated by spaces). Mixing different read
89 types is not yet supported.
90
91 You must provide an estimate of the genome size as input,
92 which is used for solid k-mers selection. The estimate could
93 be rough (e.g. withing 0.5x-2x range) and does not affect
94 the other assembly stages. Standard size modificators are
95 supported (e.g. 5m or 2.6g).
96
97 ]]></help>
98 <expand macro="citations" />
99 </tool>