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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/disco/ commit d9fc31caa31f1f0c63a0dd5ffe136d765d607080"
author iuc
date Sun, 18 Apr 2021 17:48:28 +0000
parents 6d447ebb2bf4
children
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1:6de3e77073ad 2:dfefaf2bab95
1 <tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.0"> 1 <tool id="disco" name="DISCO" version="@WRAPPER_VERSION@.1" profile="20.01">
2 <description>to assemble metagenomics data using an overlap-layout-consensus (OLC) approach</description> 2 <description>to assemble metagenomics data using an overlap-layout-consensus (OLC) approach</description>
3 <macros> 3 <macros>
4 <token name="@WRAPPER_VERSION@">1.2</token> 4 <token name="@WRAPPER_VERSION@">1.2</token>
5 <xml name="assembly_params"> 5 <xml name="assembly_params">
6 <param argument="minSequenceLengthTobePrinted" type="integer" value="1000" min="0" label="Minimum length of contigs or scaffolds to be printed"/> 6 <param argument="minSequenceLengthTobePrinted" type="integer" value="1000" min="0" label="Minimum length of contigs or scaffolds to be printed"/>
18 </xml> 18 </xml>
19 </macros> 19 </macros>
20 <requirements> 20 <requirements>
21 <requirement type="package" version="@WRAPPER_VERSION@">disco</requirement> 21 <requirement type="package" version="@WRAPPER_VERSION@">disco</requirement>
22 </requirements> 22 </requirements>
23 <version_command>runDisco.sh --version</version_command> 23 <version_command>echo @WRAPPER_VERSION@</version_command>
24 <command detect_errors="exit_code"><![CDATA[ 24 <command detect_errors="exit_code"><![CDATA[
25 #if $input_cond.library_type == "single"
26 #for i, e in enumerate($input_cond.inS)
27 cp '$e'
28 #if $e.ext.endswith(".gz")
29 input_${i}.fastq.gz &&
30 #else
31 input_${i}.fastq &&
32 #end if
33 #end for
34 #else
35 #if $input_cond.paired_input.type == "separated"
36 #if $input_cond.paired_input.in1.ext.endswith(".gz")
37 cp '$input_cond.paired_input.in1' forward.fastq.gz &&
38 cp '$input_cond.paired_input.in2' reverse.fastq.gz &&
39 #else
40 cp '$input_cond.paired_input.in1' forward.fastq &&
41 cp '$input_cond.paired_input.in2' reverse.fastq &&
42 #end if
43 #else
44 #for i, e in enumerate($input_cond.paired_input.inP)
45 cp '$e'
46 #if $e.ext.endswith(".gz")
47 input_${i}.fastq.gz &&
48 #else
49 input_${i}.fastq &&
50 #end if
51 #end for
52 #end if
53 #end if
25 runDisco.sh 54 runDisco.sh
26 -n \${GALAXY_SLOTS:-4} 55 -n \${GALAXY_SLOTS:-4}
27 -m \${DISCO_MAX_MEMORY:-4} 56 -m \${DISCO_MAX_MEMORY:-4}
28 -d . 57 -d .
29 -o disco 58 -o disco
30 #if $input.library_type == "single" 59 #if $input_cond.library_type == "single"
31 -inS '$input.inS' 60 -inS \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//')
32 #else 61 #else
33 #if $input.paired_input.type == "separated" 62 #if $input_cond.paired_input.type == "separated"
34 -in1 '$input.paired_input.in1' 63 #if $input_cond.paired_input.in1.ext.endswith(".gz")
35 -in2 '$input.paired_input.in2' 64 -in1 forward.fastq.gz
65 -in2 reverse.fastq.gz
66 #else
67 -in1 forward.fastq
68 -in2 reverse.fastq
69 #end if
36 #else 70 #else
37 -inP '$input.paired_input.inP' 71 -inP \$(find . -name "*fastq*" -print | tr '\n' ',' | sed 's/,$//')
38 #end if 72 #end if
39 #end if 73 #end if
40 $obg 74 $obg
41 $osg 75 $osg
42 -p '$first_assembly_iteration_params' 76 -p '$first_assembly_iteration_params'
107 minReadsCountInEdgeToBe1MinFlow = $third_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow 141 minReadsCountInEdgeToBe1MinFlow = $third_assembly_iter_param.minReadsCountInEdgeToBe1MinFlow
108 minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow 142 minEdgeLengthToBe1MinFlow = $third_assembly_iter_param.minEdgeLengthToBe1MinFlow
109 ]]></configfile> 143 ]]></configfile>
110 </configfiles> 144 </configfiles>
111 <inputs> 145 <inputs>
112 <conditional name="input"> 146 <conditional name="input_cond">
113 <param name="library_type" type="select" label="Type of library?"> 147 <param name="library_type" type="select" label="Type of library?">
114 <option value="single">Single-end reads</option> 148 <option value="single">Single-end reads</option>
115 <option value="paired">Paired-end reads</option> 149 <option value="paired">Paired-end reads</option>
116 </param> 150 </param>
117 <when value="single"> 151 <when value="single">
118 <param argument="-inS" type="data" format="fastq,fasta" multiple="true" label="Single-read files"/> 152 <param argument="-inS" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Single-read files"/>
119 </when> 153 </when>
120 <when value="paired"> 154 <when value="paired">
121 <conditional name="paired_input"> 155 <conditional name="paired_input">
122 <param name="type" type="select" label="Type of library?"> 156 <param name="type" type="select" label="Type of library?">
123 <option value="separated">Separated forward/reverse paired-read files</option> 157 <option value="separated">Separated forward/reverse paired-read files</option>
124 <option value="interleaved">Interleaved paired-read files</option> 158 <option value="interleaved">Interleaved paired-read files</option>
125 </param> 159 </param>
126 <when value="separated"> 160 <when value="separated">
127 <param argument="-in1" type="data" format="fastq,fasta" label="Forward read file" /> 161 <param argument="-in1" type="data" format="fastq,fastq.gz,fasta" label="Forward read file" />
128 <param argument="-in2" type="data" format="fastq,fasta" label="Reverse read file" /> 162 <param argument="-in2" type="data" format="fastq,fastq.gz,fasta" label="Reverse read file" />
129 </when> 163 </when>
130 <when value="interleaved"> 164 <when value="interleaved">
131 <param argument="-inP" type="data" format="fastq,fasta" multiple="true" label="Interleaved paired-read files" /> 165 <param argument="-inP" type="data" format="fastq,fastq.gz,fasta" multiple="true" label="Interleaved paired-read files" />
132 </when> 166 </when>
133 </conditional> 167 </conditional>
134 </when> 168 </when>
135 </conditional> 169 </conditional>
136 <param argument="-obg" type="boolean" truevalue="-obg" falsevalue="" checked="false" label="Only build overlap graph?"/> 170 <param argument="-obg" type="boolean" truevalue="-obg" falsevalue="" checked="false" label="Only build overlap graph?"/>
170 <discover_datasets pattern="disco_Graph_(?P&lt;designation&gt;.+)\.gfa2" format="txt" directory="assembly" /> 204 <discover_datasets pattern="disco_Graph_(?P&lt;designation&gt;.+)\.gfa2" format="txt" directory="assembly" />
171 </collection> 205 </collection>
172 </outputs> 206 </outputs>
173 <tests> 207 <tests>
174 <test> 208 <test>
175 <conditional name="input"> 209 <conditional name="input_cond">
176 <param name="library_type" value="paired"/> 210 <param name="library_type" value="paired"/>
177 <conditional name="paired_input"> 211 <conditional name="paired_input">
178 <param name="type" value="separated"/> 212 <param name="type" value="separated"/>
179 <param name="in1" value="ecoli_1K_1.fq"/> 213 <param name="in1" value="ecoli_1K_1.fq"/>
180 <param name="in2" value="ecoli_1K_2.fq"/> 214 <param name="in2" value="ecoli_1K_2.fq"/>
263 <output_collection name="gfa2_graphs" type="list"> 297 <output_collection name="gfa2_graphs" type="list">
264 <element name="1" file="test1_graph_1.gfa2" compare="sim_size" delta="6000"/> 298 <element name="1" file="test1_graph_1.gfa2" compare="sim_size" delta="6000"/>
265 </output_collection> 299 </output_collection>
266 </test> 300 </test>
267 <test> 301 <test>
268 <conditional name="input"> 302 <conditional name="input_cond">
269 <param name="library_type" value="paired"/> 303 <param name="library_type" value="paired"/>
270 <conditional name="paired_input"> 304 <conditional name="paired_input">
271 <param name="type" value="interleaved"/> 305 <param name="type" value="interleaved"/>
272 <param name="inP" value="ecoli_1K_interleaved.fq,ecoli_1K_interleaved.fq"/> 306 <param name="inP" value="ecoli_1K_interleaved.fq,ecoli_1K_interleaved.fq"/>
273 </conditional> 307 </conditional>
331 </output> 365 </output>
332 <output name="contigs" value="test2_contigs.fasta" compare="sim_size" delta="5"/> 366 <output name="contigs" value="test2_contigs.fasta" compare="sim_size" delta="5"/>
333 <output name="scaffolds" value="test2_scaffolds.fasta" compare="sim_size" delta="5"/> 367 <output name="scaffolds" value="test2_scaffolds.fasta" compare="sim_size" delta="5"/>
334 </test> 368 </test>
335 <test> 369 <test>
336 <conditional name="input"> 370 <conditional name="input_cond">
337 <param name="library_type" value="single"/> 371 <param name="library_type" value="single"/>
338 <param name="inS" value="ecoli_1K_1.fq"/> 372 <param name="inS" value="ecoli_1K_1.fq.gz" ftype="fastq.gz"/>
339 </conditional> 373 </conditional>
340 <param name="obg" value=""/> 374 <param name="obg" value=""/>
341 <param name="osg" value=""/> 375 <param name="osg" value=""/>
342 <param name="MinOverlap4BuildGraph" value="20"/> 376 <param name="MinOverlap4BuildGraph" value="20"/>
343 <param name="log" value="false"/> 377 <param name="log" value="false"/>
391 </test> 425 </test>
392 </tests> 426 </tests>
393 <help><![CDATA[ 427 <help><![CDATA[
394 DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for computer clusters in a hybrid architecture that integrated shared-memory multi-threading, point-to-point message passing, and remote direct memory access. The assembly and scaffolding were performed using an iterative overlap graph approach. 428 DISCO is a multi threaded and multiprocess distributed memory overlap-layout-consensus (OLC) metagenome assembler. Disco was developed as a scalable assembler to assemble large metagenomes from billions of Illumina sequencing reads of complex microbial communities. Disco was parallelized for computer clusters in a hybrid architecture that integrated shared-memory multi-threading, point-to-point message passing, and remote direct memory access. The assembly and scaffolding were performed using an iterative overlap graph approach.
395 429
396 The detailed user manual of the assembler and how to use it to acheive best results is provided here: http://disco.omicsbio.org/user-manual. This is a quick start guide generally for developers and testers. Users with limited experience with genome assembly are advised to use the user manual. 430 The detailed user manual of the assembler and how to use it to acheive best results is provided here:
431 http://disco.omicsbio.org/user-manual. This is a quick start guide generally for developers and testers. Users with limited experience with genome assembly are advised to use the user manual.
397 ]]></help> 432 ]]></help>
398 <citations> 433 <citations>
399 </citations> 434 </citations>
400 </tool> 435 </tool>