Mercurial > repos > mvdbeek > wtdbg2
comparison wtdbg2.xml @ 1:fe60b4299555 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
author | mvdbeek |
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date | Mon, 26 Nov 2018 09:10:05 -0500 |
parents | 7bb3cf8b9a5d |
children | 79430547460a |
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0:7bb3cf8b9a5d | 1:fe60b4299555 |
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10 <version_command>wtdbg2 -V</version_command> | 10 <version_command>wtdbg2 -V</version_command> |
11 <command detect_errors="exit_code"><![CDATA[ | 11 <command detect_errors="exit_code"><![CDATA[ |
12 wtdbg2 -t \${GALAXY_SLOTS:-1} | 12 wtdbg2 -t \${GALAXY_SLOTS:-1} |
13 -i '$inputs' | 13 -i '$inputs' |
14 -fo prefix | 14 -fo prefix |
15 #if $preset | 15 #if $preset.select_preset != 'manual' |
16 -x '$preset.select_preset' | 16 -x '$preset.select_preset' |
17 #else | 17 #else |
18 -k $preset.kmer_length | 18 -k $preset.kmer_length |
19 -p $preset.hpc_kmer_length | 19 -p $preset.hpc_kmer_length |
20 -K $preset.high_freq_kmer | 20 -K $preset.high_freq_kmer |
38 ]]></command> | 38 ]]></command> |
39 <inputs> | 39 <inputs> |
40 <param name="inputs" type="data" format="fasta,fastq,fasta.gz,fastq.gz" help="Select input reads"/> | 40 <param name="inputs" type="data" format="fasta,fastq,fasta.gz,fastq.gz" help="Select input reads"/> |
41 <conditional name="preset"> | 41 <conditional name="preset"> |
42 <param name="select_preset" type="select"> | 42 <param name="select_preset" type="select"> |
43 <option value="rsII/rs">PacBio RSII (-p 21 -S 4 -s 0.05 -L 5000)</option> | 43 <option value="rsII">PacBio RSII (-p 21 -S 4 -s 0.05 -L 5000)</option> |
44 <option value="sequel/sq">Pacbio Sequel (-p 0 -k 15 -AS 2 -s 0.05 -L 5000)</option> | 44 <option value="sequel">Pacbio Sequel (-p 0 -k 15 -AS 2 -s 0.05 -L 5000)</option> |
45 <option value="nanopore/ont">Nanopore (-p 19 -AS 2 -s 0.05 -L 5000)</option> | 45 <option value="nanopore">Nanopore (-p 19 -AS 2 -s 0.05 -L 5000)</option> |
46 <option value="corrected/ccs">Corrected Reads (-p 0 -k 19 -AS 4 -s 0.5 -L 5000)</option> | 46 <option value="corrected">Corrected Reads (-p 0 -k 19 -AS 4 -s 0.5 -L 5000)</option> |
47 <option value="manual">Specify Options</option> | 47 <option value="manual">Specify Options</option> |
48 </param> | 48 </param> |
49 <when value="rsII/rs"> | 49 <when value="rsII"> |
50 </when> | 50 </when> |
51 <when value="sequel/sq"> | 51 <when value="sequel"> |
52 </when> | 52 </when> |
53 <when value="nanopore/ont"> | 53 <when value="nanopore"> |
54 </when> | 54 </when> |
55 <when value="corrected/ccs"> | 55 <when value="corrected"> |
56 </when> | 56 </when> |
57 <when value="manual"> | 57 <when value="manual"> |
58 <param name="kmer_length" argument="-k" type="integer" value="0" min="0" max="25" label="kmer fsize"/> | 58 <param name="kmer_length" argument="-k" type="integer" value="0" min="0" max="25" label="kmer fsize"/> |
59 <param name="hpc_kmer_length" argument="-p" type="integer" value="0" min="0" max="25" label="kmer psize"/> | 59 <param name="hpc_kmer_length" argument="-p" type="integer" value="0" min="0" max="25" label="kmer psize"/> |
60 <param name="high_freq_kmer" argument="-K" type="float" value="1000.05" label="Filter high frequency kmers, maybe repetitive" help=">= 1000 and indexing >= (1 - 0.05) * total_kmers_count"/> | 60 <param name="high_freq_kmer" argument="-K" type="float" value="1000.05" label="Filter high frequency kmers, maybe repetitive" help=">= 1000 and indexing >= (1 - 0.05) * total_kmers_count"/> |
78 <data name="polished_consensus" format="fasta" from_work_dir="prefix.ctg.lay.2nd.fa"/> | 78 <data name="polished_consensus" format="fasta" from_work_dir="prefix.ctg.lay.2nd.fa"/> |
79 </outputs> | 79 </outputs> |
80 <tests> | 80 <tests> |
81 <test> | 81 <test> |
82 <param name="inputs" value="ecoli-reads.fasta" ftype="fasta"/> | 82 <param name="inputs" value="ecoli-reads.fasta" ftype="fasta"/> |
83 <param name="preset|select_preset" value="rsII/rs"/> | 83 <param name="preset|select_preset" value="rsII"/> |
84 <output name="contigs" value="contigs.txt"/> | 84 <output name="contigs" value="contigs.txt"/> |
85 <output name="consensus" value="consensus.fa"/> | 85 <output name="consensus" value="consensus.fa"/> |
86 <output name="polished_consensus" value="polished_consensus.fa"/> | 86 <output name="polished_consensus" value="polished_consensus.fa"/> |
87 </test> | 87 </test> |
88 </tests> | 88 </tests> |