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comparison spades.xml @ 5:909c315b656d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades commit 9d484642914b581ce35f254466b849d3c4c2c06c-dirty
author iuc
date Wed, 01 Mar 2017 15:33:26 -0500
parents 35cb17bd8bf9
children 65c2d63fcbe6
comparison
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4:35cb17bd8bf9 5:909c315b656d
1 <tool id="spades" name="spades" version="1.4"> 1 <tool id="spades" name="SPAdes" version="3.9.0">
2 <description>SPAdes genome assembler for regular and single-cell projects</description> 2 <description>genome assembler for regular and single-cell projects</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="3.9.0">spades</requirement> 4 <requirement type="package" version="3.9.0">spades</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="perl">spades.pl 6 <stdio>
7 $out_contigs 7 <exit_code range="1:" />
8 $out_contig_stats 8 </stdio>
9 $out_scaffolds 9 <command>
10 $out_scaffold_stats 10 <![CDATA[
11 $out_log 11 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output
12 12 spades.py -o . --disable-gzip-output $sc $onlyassembler $careful -t \${GALAXY_SLOTS:-16}
13 ## if the first library file is a paired-collection, use the key as the name 13 #if not $kmer_choice.auto_kmer_choice:
14 #if $libraries[0].files[0].file_type.type == "paired-collection": 14 -k "$kmer_choice.kmers"
15 $libraries[0].files[0].file_type.fastq_collection.name
16 #else:
17 NODE
18 #end if 15 #end if
19 ## A real command looks like: spades.py -k 21,33,55,77,99,127 --careful -1 Y.fastq.gz -2 X.fastq.gz -t 24 -o output 16 #if $cov.state == "auto":
20 spades.py 17 --cov-cutoff 'auto'
21 ## Forces unzipped output, faster 18 #elif $cov.state == "value":
22 --disable-gzip-output 19 --cov-cutoff '$cov.cutoff'
23 $sc
24 $onlyassembler
25 $careful
26 -t \${GALAXY_SLOTS:-16}
27
28 #if not $kmer_choice.auto_kmer_choice:
29 -k "$kmer_choice.kmers"
30 #else
31
32 #end if 20 #end if
33
34 #if $cov.state == "auto":
35 --cov-cutoff 'auto'
36 #elif $cov.state == "value":
37 --cov-cutoff '$cov.cutoff'
38 #end if
39
40 $iontorrent 21 $iontorrent
41
42 ## Sequence files, libraries 22 ## Sequence files, libraries
43 #for $i, $library in enumerate( $libraries ) 23 #for $i, $library in enumerate( $libraries, start=1 )
44 #set num=$i+1 24 #if str( $library.lib_type ) == "paired_end":
45 #if str( $library.lib_type ) == "paired_end": 25 #set prefix = 'pe'
46 #set prefix = 'pe' 26 #elif str( $library.lib_type ) == "mate_paired":
47 #elif str( $library.lib_type ) == "mate_paired": 27 #set prefix = 'mp'
48 #set prefix = 'mp' 28 #elif str( $library.lib_type ) == "nxmate_paired":
49 #elif str( $library.lib_type ) == "nxmate_paired": 29 #set prefix = 'nxmate'
50 #set prefix = 'nxmate' 30 #else:
51 #else: 31 #set prefix = 'hqmp'
52 #set prefix = 'hqmp' 32 #end if
53 #end if 33 --$prefix$i-$library.orientation
54 --$prefix$num-$library.orientation 34 #for $file in $library.files
55 #for $file in $library.files 35 #if $file.file_type.type == "separate"
56 #if $file.file_type.type == "separate" 36 --$prefix$i-1 fastq:$file.file_type.fwd_reads
57 --$prefix$num-1 fastq:$file.file_type.fwd_reads 37 --$prefix$i-2 fastq:$file.file_type.rev_reads
58 --$prefix$num-2 fastq:$file.file_type.rev_reads 38 #elif $file.file_type.type == "interleaved"
59 #elif $file.file_type.type == "interleaved" 39 --$prefix$i-12 fastq:$file.file_type.interleaved_reads
60 --$prefix$num-12 fastq:$file.file_type.interleaved_reads 40 #elif $file.file_type.type == "unpaired"
61 #elif $file.file_type.type == "unpaired" 41 --$prefix$i-s fastq:$file.file_type.unpaired_reads
62 --$prefix$num-s fastq:$file.file_type.unpaired_reads 42 #elif $file.file_type.type == "paired-collection"
63 #elif $file.file_type.type == "paired-collection" 43 --$prefix$i-1 fastq:$file.file_type.fastq_collection.forward
64 --$prefix$num-1 fastq:$file.file_type.fastq_collection.forward 44 --$prefix$i-2 fastq:$file.file_type.fastq_collection.reverse
65 --$prefix$num-2 fastq:$file.file_type.fastq_collection.reverse 45 #end if
66 #end if 46 #end for
67 #end for 47 #end for
68 #end for 48 #for $read in $pacbio_reads:
69 ## PacBio reads 49 #if $read:
70 #for $i, $pacbiolib in enumerate( $pacbio ) 50 --pacbio fastq:$read
71 --pacbio fastq:$pacbiolib.pacbio_reads 51 #end if
72 #end for 52 #end for
73 ## Nanopore 53 #for $read in $nanopore_reads:
74 #for $i, $nanoporelib in enumerate( $nanopore ) 54 #if $read:
75 --nanopore fastq:$nanoporelib.nanopore_reads 55 --nanopore fastq:$read
76 #end for 56 #end if
77 ## Sanger 57 #end for
78 #for $i, $sangerlib in enumerate( $sanger ) 58 #for $read in $sanger_reads:
79 --sanger $sangerlib.file_type.type:$sangerlib.file_type.sanger_reads 59 #if $read:
80 #end for 60 --sanger $read.extension:$read
81 ## Contigs 61 #end if
82 #for $i, $trustedcontigs in enumerate( $trustedcontigs ) 62 #end for
83 --trusted-contigs $trustedcontigs.file_type.type:$trustedcontigs.file_type.trusted_contigs 63 #for $contig in $trusted_contigs:
84 #end for 64 #if $contig:
85 #for $i, $untrustedcontigs in enumerate( $untrustedcontigs ) 65 --trusted-contigs $contig.extension:$contig
86 --untrusted-contigs $untrustedcontigs.file_type.type:$untrustedcontigs.file_type.untrusted_contigs 66 #end if
87 #end for 67 #end for
88 </command> 68 #for $contig in $untrusted_contigs:
89 <inputs> 69 #if $contig:
90 <param name="sc" type="boolean" truevalue="--sc" falsevalue="" label="Single-cell?" help="This option is required for MDA (single-cell) data."> 70 --untrusted-contigs $contig.extension:$contig
91 <option value="false">No</option> 71 #end if
92 <option value="true">Yes</option> 72 #end for
93 </param> 73 ]]>
94 <param name="onlyassembler" type="boolean" truevalue="--only-assembler" falsevalue="" checked="False" label="Run only assembly? (without read error correction)" /> 74 </command>
95 <param name="careful" type="boolean" truevalue="--careful" falsevalue="" checked="True" label="Careful correction?" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector – a post processing tool, which uses BWA tool (comes with SPAdes)." /> 75 <inputs>
96 <conditional name="kmer_choice"> 76 <param argument="--sc" falsevalue="" help="This option is required for MDA (single-cell) data." label="Single-cell?" name="sc" truevalue="--sc" type="boolean">
97 <param name="auto_kmer_choice" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Automatically choose k-mer values" help="k-mer choices can be chosen by SPAdes instead of being entered manually" /> 77 <option value="false">No</option>
98 <when value="false"> 78 <option value="true">Yes</option>
99 <param name="kmers" type="text" label="K-mers to use, separated by commas" value="21,33,55" help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." /> 79 </param>
100 </when> 80 <param argument="--only-assembler" checked="False" falsevalue="" label="Run only assembly? (without read error correction)" name="onlyassembler" truevalue="--only-assembler" type="boolean" />
101 <when value="true"> </when> 81 <param argument="----careful" checked="True" falsevalue="" help="Tries to reduce number of mismatches and short indels. Also runs MismatchCorrector &#8211; a post processing tool, which uses BWA tool (comes with SPAdes)." label="Careful correction?" name="careful" truevalue="--careful" type="boolean" />
102 </conditional> 82 <conditional name="kmer_choice">
103 <conditional name="cov"> 83 <param checked="False" falsevalue="false" help="k-mer choices can be chosen by SPAdes instead of being entered manually" label="Automatically choose k-mer values" name="auto_kmer_choice" truevalue="true" type="boolean" />
104 <param name="state" type="select" label="Coverage Cutoff"> 84 <when value="false">
105 <option value="off">Off</option> 85 <param help="Comma-separated list of k-mer sizes to be used (all values must be odd, less than 128, listed in ascending order, and smaller than the read length). The default value is 21,33,55." label="K-mers to use, separated by commas" name="kmers" type="text" value="21,33,55" />
106 <option value="value">User Specific</option> 86 </when>
107 <option value="auto">Auto</option> 87 <when value="true" />
108 </param> 88 </conditional>
109 <when value="off"> 89 <conditional name="cov">
110 </when> 90 <param label="Coverage Cutoff" name="state" type="select">
111 <when value="value"> 91 <option value="off">Off</option>
112 <param name="cutoff" type="float" label="Coverage cutoff value" value="" help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" /> 92 <option value="value">User Specific</option>
113 </when> 93 <option value="auto">Auto</option>
114 <when value="auto"> 94 </param>
115 </when> 95 <when value="off" />
116 </conditional> 96 <when value="value">
117 97 <param help="coverage cutoff value (a positive float number, or 'auto', or 'off') [default: 'off']" label="Coverage cutoff value" name="cutoff" type="float" value="" />
118 98 </when>
119 99 <when value="auto" />
120 <param name="iontorrent" type="boolean" truevalue="--iontorrent" falsevalue="" checked="False" label="Libraries are IonTorrent reads?" /> 100 </conditional>
121 <!-- Reads --> 101 <param checked="False" falsevalue="" label="Libraries are IonTorrent reads?" name="iontorrent" truevalue="--iontorrent" type="boolean" />
122 <repeat name="libraries" title="Libraries" min="1" help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided."> 102 <repeat help="It is not possible to specify only mate-pair libraries. Scaffolds are not produced if neither a paired-end nor a mate-pair library is provided." min="1" name="libraries" title="Libraries">
123 <param name="lib_type" type="select" label="Library type"> 103 <param label="Library type" name="lib_type" type="select">
124 <option value="paired_end">Paired-end / Single reads</option> 104 <option value="paired_end">Paired-end / Single reads</option>
125 <option value="mate_paired">Mate pairs</option> 105 <option value="mate_paired">Mate pairs</option>
126 <option value="high_mate_paired">High Quality Mate pairs</option> 106 <option value="high_mate_paired">High Quality Mate pairs</option>
127 <option value="nxmate_paired">Lucigen NxMate pairs</option> 107 <option value="nxmate_paired">Lucigen NxMate pairs</option>
128 </param> 108 </param>
129 <param name="orientation" type="select" label="Orientation"> 109 <param label="Orientation" name="orientation" type="select">
130 <option value="fr" selected="true">-> &lt;- (fr)</option> 110 <option selected="true" value="fr"><![CDATA[-> <- (fr)]]></option>
131 <option value="rf">&lt;- -> (rf)</option> 111 <option value="rf"><![CDATA[<- -> (rf)]]></option>
132 <option value="ff">-> -> (ff)</option> 112 <option value="ff"><![CDATA[-> -> (ff)]]></option>
133 </param> 113 </param>
134 <repeat name="files" title="Files" min="1"> 114 <repeat min="1" name="files" title="Files">
135 <conditional name="file_type"> 115 <conditional name="file_type">
136 <param name="type" type="select" label="Select file format"> 116 <param label="Select file format" name="type" type="select">
137 <option value="separate">Separate input files</option> 117 <option value="separate">Separate input files</option>
138 <option value="interleaved">Interleaved files</option> 118 <option value="interleaved">Interleaved files</option>
139 <option value="unpaired">Unpaired/Single reads</option> 119 <option value="unpaired">Unpaired/Single reads</option>
140 <option value="paired-collection">Paired List Collection</option> 120 <option value="paired-collection">Paired List Collection</option>
141 </param> 121 </param>
142 <when value="separate"> 122 <when value="separate">
143 <param name="fwd_reads" type="data" format="fastq" label="Forward reads" help="FASTQ format" /> 123 <param format="fastq" help="FASTQ format" label="Forward reads" name="fwd_reads" type="data" />
144 <param name="rev_reads" type="data" format="fastq" label="Reverse reads" help="FASTQ format" /> 124 <param format="fastq" help="FASTQ format" label="Reverse reads" name="rev_reads" type="data" />
145 </when> 125 </when>
146 <when value="interleaved"> 126 <when value="interleaved">
147 <param name="interleaved_reads" type="data" format="fastq" label="Interleaved paired reads" help="FASTQ format" /> 127 <param format="fastq" help="FASTQ format" label="Interleaved paired reads" name="interleaved_reads" type="data" />
148 </when> 128 </when>
149 <when value="unpaired"> 129 <when value="unpaired">
150 <param name="unpaired_reads" type="data" format="fastq" label="Unpaired reads" help="FASTQ format" /> 130 <param format="fastq" help="FASTQ format" label="Unpaired reads" name="unpaired_reads" type="data" />
151 </when> 131 </when>
152 <when value="paired-collection"> 132 <when value="paired-collection">
153 <param name="fastq_collection" type="data_collection" label="Paired-end reads collection" optional="false" format="fastq" collection_type="paired" help="FASTQ format" /> 133 <param collection_type="paired" format="fastq" help="FASTQ format" label="Paired-end reads collection" name="fastq_collection" optional="false" type="data_collection" />
154 </when> 134 </when>
155 </conditional> 135 </conditional>
156 </repeat> 136 </repeat>
157 </repeat> 137 </repeat>
158 <!-- PacBio --> 138 <param optional="true" format="fastq" label="PacBio CLR reads" multiple="true" name="pacbio_reads" type="data" />
159 <repeat name="pacbio" title="PacBio CLR reads"> 139 <param optional="true" format="fastq" label="Nanopore reads" multiple="true" name="nanopore_reads" type="data" />
160 <param name="pacbio_reads" type="data" format="fastq" label="PacBio CLR reads." help="FASTQ format. For PacBio pre-corrected or CCS reads, use single reads above." /> 140 <param optional="true" format="fasta,fastq" label="Sanger reads" multiple="true" name="sanger_reads" type="data" />
161 </repeat> 141 <param optional="true" format="fasta,fastq" label="Trusted contigs" multiple="true" name="trusted_contigs" type="data" />
162 <!-- Nanopore --> 142 <param optional="true" format="fasta,fastq" label="Untrusted contigs" multiple="true" name="untrusted_contigs" type="data" />
163 <repeat name="nanopore" title="Nanopore reads"> 143 </inputs>
164 <param name="nanopore_reads" type="data" format="fastq" label="Nanopore reads." help="FASTQ format. For Nanopore, use single reads above." /> 144 <outputs>
165 </repeat> 145 <data format="fasta" from_work_dir="contigs.fasta" label="SPAdes contigs (fasta)" name="out_contigs" />
166 <!-- Sanger --> 146 <data format="fasta" from_work_dir="scaffolds.fasta" label="SPAdes scaffolds (fasta)" name="out_scaffolds" />
167 <repeat name="sanger" title="Sanger reads"> 147 <data format="txt" from_work_dir="spades.log" label="SPAdes log" name="out_log" />
168 <conditional name="file_type"> 148 </outputs>
169 <param name="type" type="select" label="Select file format" help="No read correction is done on Sanger reads, no need to provide quality information."> 149 <tests>
170 <option value="fasta">fasta</option> 150 <test>
171 <option value="fastq">fastq</option> 151 <param name="sc" value="false" />
172 </param> 152 <param name="careful" value="false" />
173 <when value="fasta"> 153 <param name="kmers" value="33" />
174 <param name="sanger_reads" type="data" format="fasta" label="Sanger reads" help="FASTA format" /> 154 <param name="lib_type" value="paired_end" />
175 </when> 155 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
176 <when value="fastq"> 156 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
177 <param name="sanger_reads" type="data" format="fastq" label="Sanger reads" help="FASTQ format" /> 157 <output compare="re_match" file="kmer_33_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
178 </when> 158 </test>
179 </conditional> 159 <test>
180 </repeat> 160 <param name="sc" value="false" />
181 <!-- Contigs --> 161 <param name="careful" value="false" />
182 <repeat name="trustedcontigs" title="Trusted contigs" help="Reliable contigs of the same genome, which are likely to have no misassemblies and small rate of other errors (e.g. mismatches and indels). This option is not intended for contigs of the related species."> 162 <param name="auto_kmer_choice" value="true" />
183 <conditional name="file_type"> 163 <param name="lib_type" value="paired_end" />
184 <param name="type" type="select" label="Select file format"> 164 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
185 <option value="fasta">fasta</option> 165 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
186 <option value="fastq">fastq</option> 166 <output compare="re_match" file="auto_kmer_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
187 </param> 167 </test>
188 <when value="fasta"> 168 <test>
189 <param name="trusted_contigs" type="data" format="fasta" label="Trusted contigs" help="FASTA format" /> 169 <param name="sc" value="false" />
190 </when> 170 <param name="careful" value="false" />
191 <when value="fastq"> 171 <param name="kmers" value="77" />
192 <param name="trusted_contigs" type="data" format="fastq" label="Trusted contigs" help="FASTQ format" /> 172 <param name="lib_type" value="paired_end" />
193 </when> 173 <param ftype="fastq" name="fwd_reads" value="ecoli_1K_1.fq" />
194 </conditional> 174 <param ftype="fastq" name="rev_reads" value="ecoli_1K_2.fq" />
195 </repeat> 175 <output compare="re_match" file="kmer_77_output.fa" ftype="fasta" lines_diff="1" name="out_contigs" />
196 <repeat name="untrustedcontigs" title="Untrusted contigs" help="Contigs of the same genome, quality of which is average or unknown. Contigs of poor quality can be used but may introduce errors in the assembly. This option is also not intended for contigs of the related species."> 176 </test>
197 <conditional name="file_type"> 177 </tests>
198 <param name="type" type="select" label="Select file format"> 178 <help>
199 <option value="fasta">fasta</option> 179 <![CDATA[
200 <option value="fastq">fastq</option>
201 </param>
202 <when value="fasta">
203 <param name="untrusted_contigs" type="data" format="fasta" label="Untrusted contigs" help="FASTA format" />
204 </when>
205 <when value="fastq">
206 <param name="untrusted_contigs" type="data" format="fastq" label="Untrusted contigs" help="FASTQ format" />
207 </when>
208 </conditional>
209 </repeat>
210 </inputs>
211 <outputs>
212 <data name="out_contigs" format="fasta" label="SPAdes contigs (fasta)" />
213 <data name="out_contig_stats" format="tabular" label="SPAdes contig stats" />
214 <data name="out_scaffolds" format="fasta" label="SPAdes scaffolds (fasta)" />
215 <data name="out_scaffold_stats" format="tabular" label="SPAdes scaffold stats" />
216 <data name="out_log" format="txt" label="SPAdes log" />
217 </outputs>
218 <tests>
219 <test>
220 <param name="sc" value="false" />
221 <param name="careful" value="false" />
222 <param name="kmers" value="33" />
223 <param name="lib_type" value="paired_end" />
224 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
225 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
226 <output name="out_contigs" file="kmer_33_output.fa" ftype="fasta" compare="re_match" lines_diff="1" />
227 </test>
228 <test>
229 <param name="sc" value="false" />
230 <param name="careful" value="false" />
231 <param name="auto_kmer_choice" value="true" />
232 <param name="lib_type" value="paired_end" />
233 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
234 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
235 <output name="out_contigs" file="auto_kmer_output.fa" ftype="fasta" compare="re_match" lines_diff="1" />
236 </test>
237 <test>
238 <param name="sc" value="false" />
239 <param name="careful" value="false" />
240 <param name="kmers" value="77" />
241 <param name="lib_type" value="paired_end" />
242 <param name="fwd_reads" value="ecoli_1K_1.fq" ftype="fastq" />
243 <param name="rev_reads" value="ecoli_1K_2.fq" ftype="fastq" />
244 <output name="out_contigs" file="kmer_77_output.fa" ftype="fasta" compare="re_match" lines_diff="1" />
245 </test>
246 </tests>
247 <help>
248 **What it does** 180 **What it does**
249 181
250 SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes. 182 SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. See http://bioinf.spbau.ru/en/spades for more details on SPAdes.
251 183
252 This wrapper runs SPAdes 3.9, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage. 184 This wrapper runs SPAdes 3.9, collects the output, and throws away all the temporary files. It also produces a tab file with contig names, length and coverage.
253 185
254 **License** 186 **License**
255 187
256 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2. 188 SPAdes is developed by and copyrighted to Saint-Petersburg Academic University, and is released under GPLv2.
257 189
266 Original wrapper developed by Lionel Guy. 198 Original wrapper developed by Lionel Guy.
267 199
268 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes. 200 Anton Korobeynikov greatlty helped understanding how SPAdes work, and integrated handy features into SPAdes.
269 201
270 Nicola Soranzo fixed various bugs. 202 Nicola Soranzo fixed various bugs.
271 </help> 203 ]]>
204 </help>
272 <citations> 205 <citations>
273 <citation type="doi">10.1089/cmb.2012.0021</citation> 206 <citation type="doi">10.1089/cmb.2012.0021</citation>
274 </citations> 207 </citations>
275 </tool> 208 </tool>