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comparison mira3.xml @ 0:aa75dcf4cd74 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/mira3 commit b5d52d0664b01d252cf61b98be373d09f1ecc2df-dirty
author jvolkening
date Fri, 23 Aug 2019 00:30:33 -0400
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children 858504cdf67c
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-1:000000000000 0:aa75dcf4cd74
1 <tool id="mira3" name="MIRA Assembler v3" version="3.4.1.1">
2
3 <description>Assemble short/long/hybrid reads using MIRA 3.4</description>
4
5 <!-- ***************************************************************** -->
6
7 <requirements>
8 <requirement type="package" version="3.4.1.1">mira</requirement>
9 </requirements>
10
11 <!-- ***************************************************************** -->
12
13 <version_command>mira --version | perl -wnE'print "$1\n" for /This is MIRA V([\d\.]+)/g'</version_command>
14
15 <!-- ***************************************************************** -->
16
17 <command detect_errors="aggressive">
18 <![CDATA[
19
20 mira
21 --project=mira
22 --job=$job_method,$job_type,$job_quality
23 -GE:not="\${GALAXY_SLOTS:-1}"
24 #if $condBackbone.use == "true":
25 ## Can this be linked to job_method as well? If mapping we need the backbone...
26 -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
27 #end if
28 #if $condSanger.use == "true":
29 SANGER_SETTINGS
30 ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
31 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
32 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
33 ${condSanger.sanger_extra}
34 #end if
35 #if $condRoche.use == "true":
36 454_SETTINGS
37 ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
38 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
39 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
40 ${condRoche.roche_extra}
41 #end if
42 #if $condIllumina.use == "true":
43 SOLEXA_SETTINGS
44 ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
45 -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
46 ${condIllumina.solexa_extra}
47 ##TODO - Look at -LR FASTQ qual offset (fqqo)
48 #end if
49 #if $condIonTorrent.use == "true":
50 IONTOR_SETTINGS
51 ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
52 ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
53 -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
54 ${condIonTorrent.torrent_extra}
55 #end if
56
57 COMMON_SETTINGS
58 $common_extra
59
60 ##ignore warnings about long read names
61 -MI:somrnl=0
62
63 ##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
64 ##Explicitly disable formats we won't use like MAF (reduce IO)
65 -OUT:orf=$output_fasta:orc=$output_caf:ora=$output_ace:orw=$output_wig:orm=0:org=0:ors=0
66
67 ##remove_rollover_tmps, remove_tmp_directory
68 -OUT:rrot=1:rtd=1
69
70 ##put mira temp directory on local storage
71 ##NO, must run from NFS or problems with multiple jobs/same name can arise
72 ##-DI:trt=/tmp
73 -MI:sonfs=no
74 ]]>
75 </command>
76
77 <!-- ***************************************************************** -->
78
79 <inputs>
80 <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)">
81 <option value="denovo">De novo</option>
82 <option value="mapping">Mapping</option>
83 </param>
84 <param name="job_type" type="select" label="Assembly type">
85 <option value="genome">Genome</option>
86 <option value="est">EST (transcriptome)</option>
87 </param>
88 <param name="job_quality" type="select" label="Assembly quality grade">
89 <option value="accurate">Accurate</option>
90 <option value="normal">Normal (deprecated)</option>
91 <option value="draft">Draft</option>
92 </param>
93 <!-- Backbone -->
94 <conditional name="condBackbone">
95 <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly.">
96 <option value="false">No</option>
97 <option value="true">Yes</option>
98 </param>
99 <when value="false" />
100 <when value="true">
101 <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) -->
102 <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" />
103 </when>
104 </conditional>
105 <!-- Sanger -->
106 <conditional name="condSanger">
107 <param name="use" type="select" label="Sanger/Capillary reads?">
108 <option value="false">No</option>
109 <option value="true">Yes</option>
110 </param>
111 <when value="false" />
112 <when value="true">
113 <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" />
114 <param name="sanger_extra" type="text" size="100" value="" label="extra Sanger parameters for MIRA">
115 <sanitizer invalid_char="">
116 <valid initial=",string.letters,string.digits">
117 <add value=" " />
118 <add value="-" />
119 <add value=":" />
120 <add value="=" />
121 </valid>
122 </sanitizer>
123 </param>
124 </when>
125 </conditional>
126 <!-- Roche 454 -->
127 <conditional name="condRoche">
128 <param name="use" type="select" label="454 reads?">
129 <option value="false">No</option>
130 <option value="true">Yes</option>
131 </param>
132 <when value="false" />
133 <when value="true">
134 <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences -->
135 <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" />
136 <param name="roche_extra" type="text" size="100" value="" label="extra 454 parameters for MIRA">
137 <sanitizer invalid_char="">
138 <valid initial=",string.letters,string.digits">
139 <add value=" " />
140 <add value="-" />
141 <add value=":" />
142 <add value="=" />
143 </valid>
144 </sanitizer>
145 </param>
146 </when>
147 </conditional>
148 <!-- Illumina -->
149 <conditional name="condIllumina">
150 <param name="use" type="select" label="Solexa/Illumina reads?">
151 <option value="false">No</option>
152 <option value="true">Yes</option>
153 </param>
154 <when value="false" />
155 <when value="true">
156 <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" />
157 <param name="solexa_extra" type="text" size="100" value="-DP:ure=yes -AS:mrpc=100 -AL:mo=16" label="extra Illumina parameters for MIRA">
158 <sanitizer invalid_char="">
159 <valid initial=",string.letters,string.digits">
160 <add value=" " />
161 <add value="-" />
162 <add value=":" />
163 <add value="=" />
164 </valid>
165 </sanitizer>
166 </param>
167 </when>
168 </conditional>
169 <!-- Ion Torrent -->
170 <conditional name="condIonTorrent">
171 <param name="use" type="select" label="Ion Torrent reads?">
172 <option value="false">No</option>
173 <option value="true">Yes</option>
174 </param>
175 <when value="false" />
176 <when value="true">
177 <!-- TODO? Support SFF files directly, e.g. with sff_extract -->
178 <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" />
179 <param name="torrent_extra" type="text" size="100" value="" label="extra IonTorrent parameters for MIRA">
180 <sanitizer invalid_char="">
181 <valid initial=",string.letters,string.digits">
182 <add value=" " />
183 <add value="-" />
184 <add value=":" />
185 <add value="=" />
186 </valid>
187 </sanitizer>
188 </param>
189 </when>
190 </conditional>
191 <param name="common_extra" type="text" size="100" value="-CO:mr=yes:mroir=no:asir=yes -SK:mnr=no:mmhr=.2 -AS:urd=no:ard=no:sd=yes:sdlpo=no" label="extra common parameters for MIRA">
192 <sanitizer invalid_char="">
193 <valid initial=",string.letters,string.digits">
194 <add value=" " />
195 <add value="-" />
196 <add value=":" />
197 <add value="=" />
198 </valid>
199 </sanitizer>
200 </param>
201 <param name="output_fasta" type="boolean" truevalue="1" falsevalue="0" checked="yes" label="Output FASTA" />
202 <param name="output_caf" type="boolean" truevalue="1" falsevalue="0" checked="0" label="Output CAF" />
203 <param name="output_ace" type="boolean" truevalue="1" falsevalue="0" checked="0" label="Output ACE" />
204 <param name="output_wig" type="boolean" truevalue="1" falsevalue="0" checked="0" label="Output WIG" />
205 </inputs>
206
207 <!-- ***************************************************************** -->
208
209 <outputs>
210 <data name="out_log" format="txt" label="MIRA log" from_work_dir="mira_assembly/mira_d_info/mira_info_assembly.txt" />
211 <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" from_work_dir="mira_assembly/mira_d_results/mira_out.unpadded.fasta">
212 <filter>output_fasta is True</filter>
213 </data>
214 <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" from_work_dir="mira_assembly/mira_d_results/mira_out.unpadded.fasta.qual">
215 <filter>output_fasta is True</filter>
216 </data>
217 <data name="out_caf" format="txt" label="MIRA contigs (CAF)" from_work_dir="mira_assembly/mira_d_results/mira_out.caf" >
218 <filter>output_caf is True</filter>
219 </data>
220 <data name="out_ace" format="txt" label="MIRA contigs (ACE)" from_work_dir="mira_assembly/mira_d_results/mira_out.ace">
221 <filter>output_ace is True</filter>
222 </data>
223 <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" from_work_dir="mira_assembly/mira_d_results/mira_out.wig">
224 <filter>output_wig is True</filter>
225 </data>
226 </outputs>
227
228 <!-- ***************************************************************** -->
229
230 <tests>
231 <test>
232 <param name="job_method" value="denovo" />
233 <param name="job_type" value="est" />
234 <param name="job_qual" value="accurate" />
235 <param name="condBackbone|use" value="false" />
236 <param name="condSanger|use" value="true" />
237 <param name="condSanger|filename" value="tvc_mini.fastq" ftype="fastq" />
238 <param name="condRoche|use" value="false" />
239 <param name="condIllumina|use" value="false" />
240 <param name="condIonTorrent|use" value="false" />
241 <param name="output_fasta" value="true" />
242 <param name="output_caf" value="false" />
243 <param name="output_ace" value="false" />
244 <param name="output_wig" value="false" />
245 <param name="common_extra" value="" />
246 <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" />
247 </test>
248 </tests>
249
250 <!-- ***************************************************************** -->
251
252 <help>
253
254 **What it does**
255
256 Runs MIRA v3.4, collects the output, and throws away all the temporary files.
257
258 MIRA is an open source assembly tool capable of handling sequence data from
259 a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also
260 Ion Torrent).
261
262 It is particularly suited to small genomes such as bacteria.
263
264 </help>
265
266 <!-- ***************************************************************** -->
267
268 <citations>
269 <citation type="doi">10.7717/peerj.167</citation>
270 <citation type="bibtex">@ARTICLE{Chevreux1999-mira3,
271 author = {B. Chevreux and T. Wetter and S. Suhai},
272 year = {1999},
273 title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information},
274 journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)}
275 volume = {99},
276 pages = {45-56},
277 url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html}
278 }</citation>
279 </citations>
280
281 </tool>