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comparison shovill.xml @ 1:57d5928f456e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/shovill commit 0456f085bac2c88b8cbddfcf12b02776d2a0d457
author iuc
date Wed, 07 Mar 2018 02:10:01 -0500
parents 196a599ec43d
children f698c7604b3b
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0:196a599ec43d 1:57d5928f456e
1 <tool id="shovill" name="Shovill" version="0.8.0"> 1 <tool id="shovill" name="Shovill" version="0.9.0">
2 <description>Faster SPAdes assembly of Illumina reads</description> 2 <description>Faster SPAdes assembly of Illumina reads</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.8.0">shovill</requirement> 4 <requirement type="package" version="0.9.0">shovill</requirement>
5 </requirements> 5 </requirements>
6 <version_command>shovill --version</version_command> 6 <version_command>shovill --version</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 shovill 8 shovill
9 --outdir 'out' 9 --outdir 'out'
30 #end if 30 #end if
31 $adv.nocorr 31 $adv.nocorr
32 --minlen $adv.minlen 32 --minlen $adv.minlen
33 --mincov $adv.mincov 33 --mincov $adv.mincov
34 --asm $adv.asm 34 --asm $adv.asm
35 35
36 ]]></command> 36 ]]></command>
37 <inputs> 37 <inputs>
38 <conditional name="library"> 38 <conditional name="library">
39 <param name="lib_type" type="select" label="Input reads type, collection or single library" help="Select 'paired end' for a single library or 'collection' for a paired end collection"> 39 <param name="lib_type" type="select" label="Input reads type, collection or single library" help="Select 'paired end' for a single library or 'collection' for a paired end collection">
40 <option value="paired" selected="true">Paired End</option> 40 <option value="paired" selected="true">Paired End</option>
43 <when value="paired"> 43 <when value="paired">
44 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/> 44 <param name="R1" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Forward reads (R1)" help="The file of forward reads in FASTQ format"/>
45 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/> 45 <param name="R2" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Reverse reads (R2)" help="The file of reverse reads in FASTQ format"/>
46 </when> 46 </when>
47 <when value="collection"> 47 <when value="collection">
48 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/> 48 <param name="input1" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="Paired collection" help="See help section for an explanation of dataset collections"/>
49 </when> 49 </when>
50 </conditional> 50 </conditional>
51 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" /> 51 <param name="trim" argument="--trim" type="boolean" truevalue="--trim" falsevalue="" label="Trim reads" help="Use Trimmomatic to remove common adaptors first (default: OFF)" />
52 <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" /> 52 <param name="log" type="boolean" label="Output log file?" checked="true" help="Return the Shovill log file as part of the output. Default is on" />
53 <section name="adv" title="Advanced options" expanded="False"> 53 <section name="adv" title="Advanced options" expanded="False">
68 <option value="contigs" selected="true">contigs</option> 68 <option value="contigs" selected="true">contigs</option>
69 <option value="scaffolds">scaffolds</option> 69 <option value="scaffolds">scaffolds</option>
70 </param> 70 </param>
71 </section> 71 </section>
72 </inputs> 72 </inputs>
73 73
74 <outputs> 74 <outputs>
75 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" > 75 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" >
76 <filter>log</filter> 76 <filter>log</filter>
77 </data> 77 </data>
78 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/> 78 <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="out/contigs.fa"/>
79 <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/> 79 <data format="txt" name="contigs_graph" label="${tool.name} on ${on_string}: Contig Graph" from_work_dir="out/contigs.gfa"/>
80 </outputs> 80 </outputs>
81 81
82 <tests> 82 <tests>
83 <test> <!-- Test 0: Basic test --> 83 <test> <!-- Test 0: Basic test -->
84 <param name="lib_type" value="paired" /> 84 <param name="lib_type" value="paired" />
85 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" /> 85 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
86 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" /> 86 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
120 </output> 120 </output>
121 <output name="shovill_std_log" ftype="txt" > 121 <output name="shovill_std_log" ftype="txt" >
122 <assert_contents> 122 <assert_contents>
123 <has_text text="Running: seqtk"/> 123 <has_text text="Running: seqtk"/>
124 <has_text text="Running: kmc"/> 124 <has_text text="Running: kmc"/>
125 <has_text text="Running: trimmomatic"/> 125 <has_text_matching expression="Running:\s+\S+\s+trimmomatic"/>
126 <has_text text="Running: lighter"/> 126 <has_text text="Running: lighter"/>
127 <has_text text="Running: flash"/> 127 <has_text text="Running: flash"/>
128 <has_text text="Running: spades"/> 128 <has_text text="Running: spades"/>
129 <has_text text="Running: bwa index"/> 129 <has_text text="Running: bwa index"/>
130 <has_text text="Running: (bwa mem"/> 130 <has_text text="Running: (bwa mem"/>
140 140
141 Details and options: 141 Details and options:
142 - Takes paired end Illumina fastq reads 142 - Takes paired end Illumina fastq reads
143 - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF) 143 - Trim reads: Use Trimmomatic to remove common adaptors first (default: OFF)
144 - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output 144 - Output log file: If set to "Yes", tool will return Shovill's log file as part of the output
145 145
146 Advanced options: 146 Advanced options:
147 - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d') 147 - Name format: Format of output contig FASTA IDs in 'printf' style (default: 'contig%05d')
148 - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100) 148 - Depth: Sub-sample the reads to this depth. Disable with *Depth: 0* (default: 100)
149 - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '') 149 - Estimated genomesize: An estimate of the final genome size, it will autodetect if this is blank. (default: '')
150 - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '') 150 - List of kmers to use: List of K-mer sizes to use in SPAdes. Blank is AUTO. (default: '')
151 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '') 151 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '')