comparison wtdbg2.xml @ 1:fe60b4299555 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/wtdbg2 commit e2f82dabda7848017302214b99404c8466351b08
author mvdbeek
date Mon, 26 Nov 2018 09:10:05 -0500
parents 7bb3cf8b9a5d
children 79430547460a
comparison
equal deleted inserted replaced
0:7bb3cf8b9a5d 1:fe60b4299555
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>