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comparison shovill.xml @ 0:196a599ec43d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/shovill commit 1515c4b987ad6858fb6f94479fa21a25a6dc033c
author iuc
date Wed, 25 Oct 2017 03:39:03 -0400
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children 57d5928f456e
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1 <tool id="shovill" name="Shovill" version="0.8.0">
2 <description>Faster SPAdes assembly of Illumina reads</description>
3 <requirements>
4 <requirement type="package" version="0.8.0">shovill</requirement>
5 </requirements>
6 <version_command>shovill --version</version_command>
7 <command detect_errors="exit_code"><![CDATA[
8 shovill
9 --outdir 'out'
10 --cpus \${GALAXY_SLOTS:-1}
11 --ram \${SHOVILL_RAM:-4}
12 #if str($library.lib_type) == "paired"
13 --R1 '$library.R1'
14 --R2 '$library.R2'
15 #else if str($library.lib_type) == "collection"
16 --R1 '$library.input1.forward'
17 --R2 '$library.input1.reverse'
18 #end if
19 $trim
20 --namefmt "$adv.namefmt"
21 --depth '$adv.depth'
22 #if $adv.gsize
23 --gsize '$adv.gsize'
24 #end if
25 #if $adv.kmers
26 --kmers '$adv.kmers'
27 #end if
28 #if $adv.opts
29 --opts '$adv.opts'
30 #end if
31 $adv.nocorr
32 --minlen $adv.minlen
33 --mincov $adv.mincov
34 --asm $adv.asm
35
36 ]]></command>
37 <inputs>
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">
40 <option value="paired" selected="true">Paired End</option>
41 <option value="collection">Paired Collection</option>
42 </param>
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"/>
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>
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"/>
49 </when>
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)" />
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">
54 <param name="namefmt" argument="--namefmt" type="text" value="contig%05d" label="Contig name format" help="Format of contig FASTA IDs in 'printf' style (default: 'contig%05d')" >
55 <sanitizer>
56 <valid initial="string.printable" />
57 </sanitizer>
58 </param>
59 <param name="depth" argument="--depth" type="integer" value="100" label="Depth" help="Sub-sample --R1/--R2 to this depth. Disable with --depth 0 (default: 100)" />
60 <param name="gsize" argument="--gsize" type="text" value="" label="Estimated genome size" help="An estimate of the final genome size, it will autodetect if this is blank. (default: '')" />
61 <param name="kmers" argument="--kmers" type="text" value="" label="List of kmer sizes to use" help="List of K-mer sizes to use in SPAdes. Blank is AUTO. default: ''" />
62 <param name="opts" argument="--opts" type="text" value="" label="Extra SPAdes options" help="eg. --plasmid --sc ... (default: '')" />
63 <param name="nocorr" argument="--nocorr" type="boolean" truevalue="--nocorr" falsevalue="" checked="True" label="Disable post-assembly correction" help="Disable post assembly correction with pilon (default: ON)" />
64 <param name="minlen" argument="--minlen" type="integer" value="0" label="Minimum contig length" help="Minimum length of contig to be output. 0 is AUTO (default: 0)" />
65 <param name="mincov" argument="--mincov" type="integer" value="2" label="Minimum contig coverage" help="Minimum coverage to call part of a contig. 0 is AUTO (default: 2)" />
66 <param name="asm" argument="--asm" type="select" label="Spades result to correct" help="Which SPAdes output to correct for: before_rr, contigs or scaffolds. (default: 'contigs')">
67 <option value="before_rr">before_rr</option>
68 <option value="contigs" selected="true">contigs</option>
69 <option value="scaffolds">scaffolds</option>
70 </param>
71 </section>
72 </inputs>
73
74 <outputs>
75 <data name="shovill_std_log" format="txt" label="${tool.name} on ${on_string} Log file" from_work_dir="out/00-shovill.log" >
76 <filter>log</filter>
77 </data>
78 <data format="fasta" name="contigs" label="${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"/>
80 </outputs>
81
82 <tests>
83 <test> <!-- Test 0: Basic test -->
84 <param name="lib_type" value="paired" />
85 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
86 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
87 <output name="contigs" ftype="fasta">
88 <assert_contents>
89 <has_text text="&gt;contig00001"/>
90 </assert_contents>
91 </output>
92 <output name="shovill_std_log" ftype="txt" >
93 <assert_contents>
94 <has_text text="Running: seqtk"/>
95 <has_text text="Running: kmc"/>
96 <has_text text="Running: lighter"/>
97 <has_text text="User supplied --nocorr"/>
98 <has_text text="Running: flash"/>
99 <has_text text="Running: spades"/>
100 <has_text text="Done."/>
101 </assert_contents>
102 </output>
103 </test>
104 <test> <!-- Test 1: Auto everything + trim + different name format test -->
105 <param name="lib_type" value="paired" />
106 <param name="R1" value="mutant_R1.fastq" ftype="fastqsanger" />
107 <param name="R2" value="mutant_R2.fastq" ftype="fastqsanger" />
108 <param name="trim" value="true" />
109 <section name="adv">
110 <param name="depth" value="0"/>
111 <param name="minlen" value="0"/>
112 <param name="mincov" value="0"/>
113 <param name="nocorr" value="false"/>
114 <param name="namefmt" value="contig%03d"/>
115 </section>
116 <output name="contigs" ftype="fasta">
117 <assert_contents>
118 <has_text text="&gt;contig001"/>
119 </assert_contents>
120 </output>
121 <output name="shovill_std_log" ftype="txt" >
122 <assert_contents>
123 <has_text text="Running: seqtk"/>
124 <has_text text="Running: kmc"/>
125 <has_text text="Running: trimmomatic"/>
126 <has_text text="Running: lighter"/>
127 <has_text text="Running: flash"/>
128 <has_text text="Running: spades"/>
129 <has_text text="Running: bwa index"/>
130 <has_text text="Running: (bwa mem"/>
131 <has_text text="Running: _JAVA"/>
132 <has_text text="Done."/>
133 </assert_contents>
134 </output>
135 </test>
136 </tests>
137 <help><![CDATA[
138 Synopsis:
139 Faster de novo assembly pipeline for Illumina paired end reads based around Spades
140
141 Details and options:
142 - Takes paired end Illumina fastq reads
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
145
146 Advanced options:
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)
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: '')
151 - Extra SPAdes options: Extra SPAdes options eg. --plasmid --sc ... (default: '')
152 - Disable post-assembly correction: Disable post assembly correction with pilon (default: ON)
153 - Minimum contig length: Minimum length of contig to be output. 0 is AUTO (default: 0)
154 - Minimum contig coverage: Minimum coverage to call part of a contig. 0 is AUTO (default: 2)
155 - Spades result to correct: Spades result to correct: before_rr, contigs or scaffolds (default: 'contigs')
156
157 Documentation can be found at Torsten Seemann `site <https://github.com/tseemann/shovill>`_.
158 ]]></help>
159 <citations>
160 <citation type="bibtex">
161 @UNPUBLISHED{Seemann2017,
162 author = {Seemann, Torsten},
163 title = {Shovill: Faster SPAdes assembly of Illumina reads},
164 year = {2017},
165 url = {https://github.com/tseemann/shovill},
166 }
167 </citation>
168 </citations>
169 </tool>