annotate runAssembly.xml @ 2:2d86d5b112e8

Uploaded
author edward-kirton
date Thu, 14 Jul 2011 22:14:07 -0400
parents
children bf1f8bc4abe6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
1 <tool id="runAssembly" name="runAssembly" version="1.0.0" force_history_refresh='True'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
2 <description>De novo assembly of Roche/454 reads using Newbler</description>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
3 <command interpreter='perl'>runAssembly_wrapper.pl
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
4 $newbler_metrics.extra_files_path
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
5 $newbler_metrics
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
6 $read_status
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
7 $trimmed_reads_fasta
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
8 $trimmed_reads_qual
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
9 $alignment_info
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
10 $all_contigs_fasta
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
11 $all_contigs_qual
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
12 $contigs_ace
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
13 $contigs_consed_ace
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
14 $contig_graph
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
15 $pair_align
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
16 $pair_status
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
17 $scaffolds_fasta
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
18 $scaffolds_qual
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
19 $scaffolds_agp
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
20 $tag_pair_align
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
21 $trim_status
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
22 $large_contigs_fasta
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
23 $large_contigs_qual
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
24 $newbler_exe -o $newbler_metrics.extra_files_path
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
25 -cpu 8
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
26 $rip
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
27 -e $e
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
28 -mi $mi
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
29 -ml $ml
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
30 -minlen $minlen
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
31 $large
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
32 $pair
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
33 $info
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
34 $notrim
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
35 $tr
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
36 $ace
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
37 $no
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
38 $qo
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
39 $nor
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
40 $ud
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
41 -ss $ss
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
42 -sl $sl
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
43 -sc $sc
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
44 -ais $ais
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
45 -a $a
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
46 -mcf $mcf
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
47 -vs $vs
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
48 -vt $vt
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
49 -fi $fi
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
50 -fe $fe
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
51 -l $l
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
52 #for $i in $sff_paired_inputs
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
53 -p ${i.sff_paired_input}
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
54 #end for
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
55 #for $i in $sanger_paired_inputs
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
56 -p ${i.sanger_paired_input}
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
57 #end for
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
58 #for $i in $sff_inputs
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
59 ${i.sff_input}
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
60 #end for
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
61 #for $i in $sanger_inputs
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
62 ${i.sanger_input}
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
63 #end for
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
64 </command>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
65 <inputs>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
66 <!-- NEWBLER VERSION -->
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
67 <param name='newbler_exe' type='select' display='radio' label='Newbler version'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
68 <option value='/jgi/tools/454/rig-DataProcessing_2.3/bin/runAssembly'>2.3</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
69 <option value='/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runAssembly'>2.4</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
70 <option value='/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runAssembly' selected='true'>2.5</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
71 </param>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
72
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
73 <!-- READSEQ INFILES -->
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
74 <repeat name="sff_inputs" title="Unpaired Reads Sff Files">
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
75 <param name="sff_input" type="data" format="sff" label="SE Sff file"/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
76 </repeat>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
77 <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
78 <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
79 </repeat>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
80 <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
81 <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
82 </repeat>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
83 <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
84 <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
85 </repeat>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
86 <param name='paired_reads' type='select' display='radio' label='[-paired_reads] If supplying paired reads (above), do you want paired-read info?'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
87 <option value='false'>no</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
88 <option value='true'>[-paired_reads] yes</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
89 </param>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
90 <param name='pair' type='select' display='radio' label='[-pair] Output pairwise overlaps'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
91 <option value=''>no</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
92 <option value='-pair'>[-pair] yes</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
93 </param>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
94
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
95 <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"/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
96
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
97 <!-- OPTIONAL ARGUMENTS -->
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
98 <param name='mcf' type='data' format='tabular' optional='true' label='[-mcf] Specify non-default MID config file' />
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
99 <param name='fi' type='data' format='txt' optional='true' label='[-fi] Include filter file to be specified' />
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
100 <param name='fe' type='data' format='txt' optional='true' label='[-fe] Exclude filter file to be specified' />
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
101 <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)" />
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
102 <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" />
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
103
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
104 <!-- READ TRIMMING -->
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
105 <param name='minlen' type='integer' value='20' label='[-minlen] Minimum length of reads to use (15-45 allowed)'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
106 <param name='notrim' type='boolean' truevalue='-notrim' falsevalue='' checked='false' label='[-notrim] Do not perform default quality and primer trimming of input reads'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
107 <param name='tr' type='select' display='radio' label='[-tr] Output trimmed reads'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
108 <option value=''>no</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
109 <option value='-tr'>[-tr] yes</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
110 </param>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
111 <param name='nor' type='boolean' truevalue='-nor' falsevalue='' label='[-nor] Turn off the automatic rescore function for read quality scores'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
112 <param name='ud' type='boolean' truevalue='-ud' falsevalue='' label='[-ud] Treat each read separately, with no grouping of duplicates'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
113
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
114 <!-- ALIGNMENT PARAMETERS -->
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
115 <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'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
116 <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'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
117 <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'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
118 <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"/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
119 <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"/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
120 <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'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
121
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
122 <!-- ASSEMBLY OPTIONS -->
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
123 <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"/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
124 <param name='large' type='boolean' truevalue='-large' falsevalue='' checked='false' label='[-large] Check if large or complex genome'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
125
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
126 <!-- OUTPUT OPTIONS -->
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
127 <param name='no' type='select' display='radio' label='[-no] Do complete assembly'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
128 <option value=''>do complete assembly</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
129 <option value='-no'>[-no] do not assemble; do alignments only</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
130 </param>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
131 <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'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
132 <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."/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
133 <param name='rip' type='boolean' truevalue='' falsevalue='-rip' checked='false' label='[-rip] Output each read in only one contig'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
134 <param name='info' type='select' display='radio' label='Output Alignment Info'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
135 <option value='-info'>[-info] yes</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
136 <option value='-infoall'>[-infoall] yes, including 0-coverage positions</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
137 </param>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
138 <param name='ace' type='select' display='radio' label='Produce Ace assembly file'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
139 <option value=''>no</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
140 <option value='-ace'>[-ace] yes</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
141 <option value='-ace -consed'>[-consed] yes, in consed dir</option>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
142 </param>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
143 </inputs>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
144
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
145 <outputs>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
146 <data name='newbler_metrics' format='txt' />
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
147 <data name='read_status' format='tabular' label='Read Status'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
148 <data name='trimmed_reads_fasta' format='fasta' label='Trimmed Reads (Fasta)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
149 <filter>tr == '-tr'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
150 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
151 <data name='trimmed_reads_qual' format='qual454' label='Trimmed Reads (Qual)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
152 <filter>tr == '-tr'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
153 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
154 <!-- the following produced only if no != '-no' -->
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
155 <data name='alignment_info' format='tabular' label='Alignment Info'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
156 <filter>no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
157 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
158 <data name='all_contigs_fasta' format='fasta' label='All Contigs (Fasta)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
159 <filter>no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
160 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
161 <data name='all_contigs_qual' format='qual454' label='All Contigs (Qual454)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
162 <filter>no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
163 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
164 <data name='contigs_ace' format='ace' label='Contigs (Ace)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
165 <filter>ace == '-ace' and no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
166 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
167 <data name='contigs_consed_ace' format='ace' label='Contigs (Consed/Ace)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
168 <filter>ace == '-ace -consed' and no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
169 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
170
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
171 <data name='contig_graph' format='txt' label='Contig Graph'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
172 <data name='large_contigs_fasta' format='fasta' label='Large Contigs (Fasta)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
173 <filter>no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
174 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
175 <data name='large_contigs_qual' format='qual454' label='Large Contigs (Qual454)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
176 <filter>no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
177 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
178 <data name='pair_align' format='txt' label='Pairwise Alignments'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
179 <filter>pair == '-pair' and no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
180 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
181 <data name='pair_status' format='tabular' label='Paired-End Read Status'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
182 <filter>paired_reads == 'true' and no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
183 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
184 <data name='scaffolds_fasta' format='fasta' label='Scaffolds (Fasta)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
185 <filter>paired_reads == 'true' and no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
186 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
187 <data name='scaffolds_qual' format='qual454' label='Scaffolds (Qual454)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
188 <filter>paired_reads == 'true' and no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
189 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
190 <data name='scaffolds_agp' format='tabular' label='Scaffolds (Agp)'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
191 <filter>paired_reads == 'true' and no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
192 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
193 <data name='tag_pair_align' format='txt' label='Tag Pair Alignments'>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
194 <filter>pair == '-pair' and paired_reads == 'true' and no != '-no'</filter>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
195 </data>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
196 <data name='trim_status' format='tabular' label='Trim Status'/>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
197
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
198 </outputs>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
199 <help>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
200
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
201 **What it does**
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
202
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
203 Assemble (Roche/454) reads using Newbler.
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
204
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
205 Download the manual here: http://galaxy.jgi-psf.org/static/manuals/GSFLXSystemSoftwareManual_PartC_Assembler-Mapper-SFFTools.pdf
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
206
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
207 .. class:: warningmark
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
208
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
209 **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.
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
210
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
211 </help>
2d86d5b112e8 Uploaded
edward-kirton
parents:
diff changeset
212 </tool>