Mercurial > repos > edward-kirton > roche454_toolsuite

comparison roche454/runAssembly.xml @ 0:f036c7107601

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:50:32 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:f036c7107601
1 <tool id="runAssembly" name="runAssembly" version="1.0.0" force_history_refresh='True'>
2 <description>De novo assembly of Roche/454 reads using Newbler</description>
3 <command interpreter='perl'>runAssembly_wrapper.pl
4 $newbler_metrics.extra_files_path
5 $newbler_metrics
6 $read_status
7 $trimmed_reads_fasta
8 $trimmed_reads_qual
9 $alignment_info
10 $all_contigs_fasta
11 $all_contigs_qual
12 $contigs_ace
13 $contigs_consed_ace
14 $contig_graph
15 $pair_align
16 $pair_status
17 $scaffolds_fasta
18 $scaffolds_qual
19 $scaffolds_agp
20 $tag_pair_align
21 $trim_status
22 $large_contigs_fasta
23 $large_contigs_qual
24 $newbler_exe -o $newbler_metrics.extra_files_path
25 -cpu 8
26 $rip
27 -e $e
28 -mi $mi
29 -ml $ml
30 -minlen $minlen
31 $large
32 $pair
33 $info
34 $notrim
35 $tr
36 $ace
37 $no
38 $qo
39 $nor
40 $ud
41 -ss $ss
42 -sl $sl
43 -sc $sc
44 -ais $ais
45 -a $a
46 -mcf $mcf
47 -vs $vs
48 -vt $vt
49 -fi $fi
50 -fe $fe
51 -l $l
52 #for $i in $sff_paired_inputs
53 -p ${i.sff_paired_input}
54 #end for
55 #for $i in $sanger_paired_inputs
56 -p ${i.sanger_paired_input}
57 #end for
58 #for $i in $sff_inputs
59 ${i.sff_input}
60 #end for
61 #for $i in $sanger_inputs
62 ${i.sanger_input}
63 #end for
64 </command>
65 <inputs>
66 <!-- NEWBLER VERSION -->
67 <param name='newbler_exe' type='select' display='radio' label='Newbler version'>
68 <option value='runAssembly' selected='true'>default</option>
69 <!-- OTHER VERSIONS MAY BE INCLUDED HERE; OR SIMPLY EDIT TO REMOVE THIS ENTIRE SECTION
70 <option value='/jgi/tools/454/rig-DataProcessing_2.3/bin/runAssembly'>2.3</option>
71 <option value='/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runAssembly'>2.4</option>
72 <option value='/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runAssembly'>2.5</option>
73 -->
74 </param>
75
76 <!-- READSEQ INFILES -->
77 <repeat name="sff_inputs" title="Unpaired Reads Sff Files">
78 <param name="sff_input" type="data" format="sff" label="SE Sff file"/>
79 </repeat>
80 <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">
81 <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>
82 </repeat>
83 <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">
84 <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>
85 </repeat>
86 <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">
87 <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>
88 </repeat>
89 <param name='paired_reads' type='select' display='radio' label='[-paired_reads] If supplying paired reads (above), do you want paired-read info?'>
90 <option value='false'>no</option>
91 <option value='true'>[-paired_reads] yes</option>
92 </param>
93 <param name='pair' type='select' display='radio' label='[-pair] Output pairwise overlaps'>
94 <option value=''>no</option>
95 <option value='-pair'>[-pair] yes</option>
96 </param>
97
98 <param name='l' type="integer" value='500' label="[-l] This option sets the minimum length for a contig to appear in the 454LargeContigs.fna file"/>
99
100 <!-- OPTIONAL ARGUMENTS -->
101 <param name='mcf' type='data' format='tabular' optional='true' label='[-mcf] Specify non-default MID config file' />
102 <param name='fi' type='data' format='txt' optional='true' label='[-fi] Include filter file to be specified' />
103 <param name='fe' type='data' format='txt' optional='true' label='[-fe] Exclude filter file to be specified' />
104 <param name='vt' type='data' format='fasta' optional='true' label="[-vt] This option specifies a vector trimming database, or FASTA file of sequences to be used to trim the ends of input reads (for cloning vectors, primers, adapters or other end sequences)" />
105 <param name='vs' type='data' format='fasta' optional='true' label="[-vs] This option specifies a vector screening database, or FASTA file of sequences to be used to screen the input reads for contaminants. Reads that completely align against the screening database are trimmed completely (so that it is not used in the computation), but otherwise the read trimpoints are not changed" />
106
107 <!-- READ TRIMMING -->
108 <param name='minlen' type='integer' value='20' label='[-minlen] Minimum length of reads to use (15-45 allowed)'/>
109 <param name='notrim' type='boolean' truevalue='-notrim' falsevalue='' checked='false' label='[-notrim] Do not perform default quality and primer trimming of input reads'/>
110 <param name='tr' type='select' display='radio' label='[-tr] Output trimmed reads'>
111 <option value=''>no</option>
112 <option value='-tr'>[-tr] yes</option>
113 </param>
114 <param name='nor' type='boolean' truevalue='-nor' falsevalue='' label='[-nor] Turn off the automatic rescore function for read quality scores'/>
115 <param name='ud' type='boolean' truevalue='-ud' falsevalue='' label='[-ud] Treat each read separately, with no grouping of duplicates'/>
116
117 <!-- ALIGNMENT PARAMETERS -->
118 <param name='ss' type='integer' value='12' label='[-ss] Seed step parameter - The number of bases between seed generation locations used in the exact k-mer matching part of the overlap detection. Allow values: 1 or greater'/>
119 <param name='sl' type='integer' value='16' label='[-sl] Seed length parameter - The number of bases used for each seed in the exact k-mer matching part of the overlap detection (i.e. the "k" value of the k-mer matching). Allowed values: 6-16'/>
120 <param name='sc' type='integer' value='1' label='[-sc] Seed count parameter - The number of seeds required in a window before an extension is made. Allowed values: 1 or greater'/>
121 <param name='ml' type="text" value='40' label="[-ml] Minimum overlap length - The minimum length of overlaps used for the pairwise alignment step. The value can either be a minimum length in bases or a percentage of read length. In the case of a percentage, simply include '%' immediately following the numeric value. Allowed values: 1 or greater"/>
122 <param name='mi' type="integer" value='90' label="[-mi] Minimum overlap identity - The percent identity of overlaps used for the pairwise alignment step. Allowed values: 0 or greater"/>
123 <param name='ais' type='integer' value='2' label='[-ais] Alignment identity score - When multiple overlaps are found, the per-overlap column identity score used to sort the overlaps for use in the progressive alignment. Allowed values: 0 or greater'/>
124
125 <!-- ASSEMBLY OPTIONS -->
126 <param name='e' type="integer" value='0' label="[-e] This option tells the assembler that the expected depth of the data is at a certain level. The assembler has been optimized for datasets in the 10-50x oversampling size, and this option helps the assembler with datasets that have a higher oversampling level. A value of 0 resets the assembler computation to use its default algorithms"/>
127 <param name='large' type='boolean' truevalue='-large' falsevalue='' checked='false' label='[-large] Check if large or complex genome'/>
128
129 <!-- OUTPUT OPTIONS -->
130 <param name='no' type='select' display='radio' label='[-no] Do complete assembly'>
131 <option value=''>do complete assembly</option>
132 <option value='-no'>[-no] do not assemble; do alignments only</option>
133 </param>
134 <param name='qo' type='boolean' truevalue='' falsevalue='-qo' checked='false' label='[-qo] Generate quick output for mapping and assembly. Disables signal distribution computation for calling consensus sequences and can decrease accuracy'/>
135 <param name='a' type="integer" value='100' label="[-a] This option sets the minimum length for a contig to appear in the 454AllContigs.fna file."/>
136 <param name='rip' type='boolean' truevalue='' falsevalue='-rip' checked='false' label='[-rip] Output each read in only one contig'/>
137 <param name='info' type='select' display='radio' label='Output Alignment Info'>
138 <option value='-info'>[-info] yes</option>
139 <option value='-infoall'>[-infoall] yes, including 0-coverage positions</option>
140 </param>
141 <param name='ace' type='select' display='radio' label='Produce Ace assembly file'>
142 <option value=''>no</option>
143 <option value='-ace'>[-ace] yes</option>
144 <option value='-ace -consed'>[-consed] yes, in consed dir</option>
145 </param>
146 </inputs>
147
148 <outputs>
149 <data name='newbler_metrics' format='txt' />
150 <data name='read_status' format='tabular' label='Read Status'/>
151 <data name='trimmed_reads_fasta' format='fasta' label='Trimmed Reads (Fasta)'>
152 <filter>tr == '-tr'</filter>
153 </data>
154 <data name='trimmed_reads_qual' format='qual454' label='Trimmed Reads (Qual)'>
155 <filter>tr == '-tr'</filter>
156 </data>
157 <!-- the following produced only if no != '-no' -->
158 <data name='alignment_info' format='tabular' label='Alignment Info'>
159 <filter>no != '-no'</filter>
160 </data>
161 <data name='all_contigs_fasta' format='fasta' label='All Contigs (Fasta)'>
162 <filter>no != '-no'</filter>
163 </data>
164 <data name='all_contigs_qual' format='qual454' label='All Contigs (Qual454)'>
165 <filter>no != '-no'</filter>
166 </data>
167 <data name='contigs_ace' format='ace' label='Contigs (Ace)'>
168 <filter>ace == '-ace' and no != '-no'</filter>
169 </data>
170 <data name='contigs_consed_ace' format='ace' label='Contigs (Consed/Ace)'>
171 <filter>ace == '-ace -consed' and no != '-no'</filter>
172 </data>
173
174 <data name='contig_graph' format='txt' label='Contig Graph'/>
175 <data name='large_contigs_fasta' format='fasta' label='Large Contigs (Fasta)'>
176 <filter>no != '-no'</filter>
177 </data>
178 <data name='large_contigs_qual' format='qual454' label='Large Contigs (Qual454)'>
179 <filter>no != '-no'</filter>
180 </data>
181 <data name='pair_align' format='txt' label='Pairwise Alignments'>
182 <filter>pair == '-pair' and no != '-no'</filter>
183 </data>
184 <data name='pair_status' format='tabular' label='Paired-End Read Status'>
185 <filter>paired_reads == 'true' and no != '-no'</filter>
186 </data>
187 <data name='scaffolds_fasta' format='fasta' label='Scaffolds (Fasta)'>
188 <filter>paired_reads == 'true' and no != '-no'</filter>
189 </data>
190 <data name='scaffolds_qual' format='qual454' label='Scaffolds (Qual454)'>
191 <filter>paired_reads == 'true' and no != '-no'</filter>
192 </data>
193 <data name='scaffolds_agp' format='tabular' label='Scaffolds (Agp)'>
194 <filter>paired_reads == 'true' and no != '-no'</filter>
195 </data>
196 <data name='tag_pair_align' format='txt' label='Tag Pair Alignments'>
197 <filter>pair == '-pair' and paired_reads == 'true' and no != '-no'</filter>
198 </data>
199 <data name='trim_status' format='tabular' label='Trim Status'/>
200
201 </outputs>
202 <help>
203
204 **What it does**
205
206 Assemble (Roche/454) reads using Newbler.
207
208 Download the manual here: http://galaxy.jgi-psf.org/static/manuals/GSFLXSystemSoftwareManual_PartC_Assembler-Mapper-SFFTools.pdf
209
210 .. class:: warningmark
211
212 **Fasta Header Format** Fasta input must provide any pairing information in the header using the expected key=value format. Use the 'Sanger tab to Newbler Fasta' tool.
213
214 </help>
215 </tool>