annotate roche454/runAssembly.xml @ 1:368a6ebebdde

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:51:04 -0400
parents f036c7107601
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
1 <tool id="runAssembly" name="runAssembly" version="1.0.0" force_history_refresh='True'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
2 <description>De novo assembly of Roche/454 reads using Newbler</description>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
3 <command interpreter='perl'>runAssembly_wrapper.pl
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
4 $newbler_metrics.extra_files_path
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
5 $newbler_metrics
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
6 $read_status
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
7 $trimmed_reads_fasta
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
8 $trimmed_reads_qual
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
9 $alignment_info
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
10 $all_contigs_fasta
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
11 $all_contigs_qual
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
12 $contigs_ace
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
13 $contigs_consed_ace
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
14 $contig_graph
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
15 $pair_align
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
16 $pair_status
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
17 $scaffolds_fasta
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
18 $scaffolds_qual
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
19 $scaffolds_agp
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
20 $tag_pair_align
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
21 $trim_status
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
22 $large_contigs_fasta
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
23 $large_contigs_qual
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
24 $newbler_exe -o $newbler_metrics.extra_files_path
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
25 -cpu 8
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
26 $rip
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
27 -e $e
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
28 -mi $mi
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
29 -ml $ml
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
30 -minlen $minlen
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
31 $large
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
32 $pair
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
33 $info
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
34 $notrim
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
35 $tr
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
36 $ace
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
37 $no
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
38 $qo
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
39 $nor
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
40 $ud
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
41 -ss $ss
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
42 -sl $sl
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
43 -sc $sc
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
44 -ais $ais
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
45 -a $a
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
46 -mcf $mcf
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
47 -vs $vs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
48 -vt $vt
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
49 -fi $fi
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
50 -fe $fe
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
51 -l $l
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
52 #for $i in $sff_paired_inputs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
53 -p ${i.sff_paired_input}
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
54 #end for
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
55 #for $i in $sanger_paired_inputs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
56 -p ${i.sanger_paired_input}
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
57 #end for
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
58 #for $i in $sff_inputs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
59 ${i.sff_input}
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
60 #end for
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
61 #for $i in $sanger_inputs
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
62 ${i.sanger_input}
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
63 #end for
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
64 </command>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
65 <inputs>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
66 <!-- NEWBLER VERSION -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
67 <param name='newbler_exe' type='select' display='radio' label='Newbler version'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
68 <option value='runAssembly' selected='true'>default</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
69 <!-- OTHER VERSIONS MAY BE INCLUDED HERE; OR SIMPLY EDIT TO REMOVE THIS ENTIRE SECTION
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
70 <option value='/jgi/tools/454/rig-DataProcessing_2.3/bin/runAssembly'>2.3</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
71 <option value='/jgi/tools/454/rig-DataProcessing_2.4pre-20091204/bin/runAssembly'>2.4</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
72 <option value='/home/copeland/local/x86_64/newbler/v2.5p1-internal-10Jun23-1/runAssembly'>2.5</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
73 -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
74 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
75
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
76 <!-- READSEQ INFILES -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
77 <repeat name="sff_inputs" title="Unpaired Reads Sff Files">
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
78 <param name="sff_input" type="data" format="sff" label="SE Sff file"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
79 </repeat>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
80 <repeat name="sanger_inputs" title="Unpaired Reads Fasta Files">
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
81 <param name="sanger_input" type="data" format="fasta" label="SE Fasta file"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
82 </repeat>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
83 <repeat name="sff_paired_inputs" title="Paired Reads Sff Files">
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
84 <param name="sff_paired_input" type="data" format="sff" label="PE Sff file"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
85 </repeat>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
86 <repeat name="sanger_paired_inputs" title="Paired Reads Fasta Files">
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
87 <param name="sanger_paired_input" type="data" format="fasta" label="PE Fasta file"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
88 </repeat>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
89 <param name='paired_reads' type='select' display='radio' label='[-paired_reads] If supplying paired reads (above), do you want paired-read info?'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
90 <option value='false'>no</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
91 <option value='true'>[-paired_reads] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
92 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
93 <param name='pair' type='select' display='radio' label='[-pair] Output pairwise overlaps'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
94 <option value=''>no</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
95 <option value='-pair'>[-pair] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
96 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
97
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
99
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
100 <!-- OPTIONAL ARGUMENTS -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
101 <param name='mcf' type='data' format='tabular' optional='true' label='[-mcf] Specify non-default MID config file' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
102 <param name='fi' type='data' format='txt' optional='true' label='[-fi] Include filter file to be specified' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
103 <param name='fe' type='data' format='txt' optional='true' label='[-fe] Exclude filter file to be specified' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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)" />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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" />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
106
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
107 <!-- READ TRIMMING -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
108 <param name='minlen' type='integer' value='20' label='[-minlen] Minimum length of reads to use (15-45 allowed)'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
109 <param name='notrim' type='boolean' truevalue='-notrim' falsevalue='' checked='false' label='[-notrim] Do not perform default quality and primer trimming of input reads'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
110 <param name='tr' type='select' display='radio' label='[-tr] Output trimmed reads'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
111 <option value=''>no</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
112 <option value='-tr'>[-tr] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
113 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
114 <param name='nor' type='boolean' truevalue='-nor' falsevalue='' label='[-nor] Turn off the automatic rescore function for read quality scores'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
115 <param name='ud' type='boolean' truevalue='-ud' falsevalue='' label='[-ud] Treat each read separately, with no grouping of duplicates'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
116
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
117 <!-- ALIGNMENT PARAMETERS -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
124
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
125 <!-- ASSEMBLY OPTIONS -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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"/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
127 <param name='large' type='boolean' truevalue='-large' falsevalue='' checked='false' label='[-large] Check if large or complex genome'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
128
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
129 <!-- OUTPUT OPTIONS -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
130 <param name='no' type='select' display='radio' label='[-no] Do complete assembly'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
131 <option value=''>do complete assembly</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
132 <option value='-no'>[-no] do not assemble; do alignments only</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
133 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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."/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
136 <param name='rip' type='boolean' truevalue='' falsevalue='-rip' checked='false' label='[-rip] Output each read in only one contig'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
137 <param name='info' type='select' display='radio' label='Output Alignment Info'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
138 <option value='-info'>[-info] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
139 <option value='-infoall'>[-infoall] yes, including 0-coverage positions</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
140 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
141 <param name='ace' type='select' display='radio' label='Produce Ace assembly file'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
142 <option value=''>no</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
143 <option value='-ace'>[-ace] yes</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
144 <option value='-ace -consed'>[-consed] yes, in consed dir</option>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
145 </param>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
146 </inputs>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
147
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
148 <outputs>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
149 <data name='newbler_metrics' format='txt' />
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
150 <data name='read_status' format='tabular' label='Read Status'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
151 <data name='trimmed_reads_fasta' format='fasta' label='Trimmed Reads (Fasta)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
152 <filter>tr == '-tr'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
153 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
154 <data name='trimmed_reads_qual' format='qual454' label='Trimmed Reads (Qual)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
155 <filter>tr == '-tr'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
156 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
157 <!-- the following produced only if no != '-no' -->
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
158 <data name='alignment_info' format='tabular' label='Alignment Info'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
159 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
160 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
161 <data name='all_contigs_fasta' format='fasta' label='All Contigs (Fasta)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
162 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
163 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
164 <data name='all_contigs_qual' format='qual454' label='All Contigs (Qual454)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
165 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
166 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
167 <data name='contigs_ace' format='ace' label='Contigs (Ace)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
168 <filter>ace == '-ace' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
169 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
170 <data name='contigs_consed_ace' format='ace' label='Contigs (Consed/Ace)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
171 <filter>ace == '-ace -consed' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
172 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
173
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
174 <data name='contig_graph' format='txt' label='Contig Graph'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
175 <data name='large_contigs_fasta' format='fasta' label='Large Contigs (Fasta)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
176 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
177 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
178 <data name='large_contigs_qual' format='qual454' label='Large Contigs (Qual454)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
179 <filter>no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
180 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
181 <data name='pair_align' format='txt' label='Pairwise Alignments'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
182 <filter>pair == '-pair' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
183 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
184 <data name='pair_status' format='tabular' label='Paired-End Read Status'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
185 <filter>paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
186 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
187 <data name='scaffolds_fasta' format='fasta' label='Scaffolds (Fasta)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
188 <filter>paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
189 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
190 <data name='scaffolds_qual' format='qual454' label='Scaffolds (Qual454)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
191 <filter>paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
192 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
193 <data name='scaffolds_agp' format='tabular' label='Scaffolds (Agp)'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
194 <filter>paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
195 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
196 <data name='tag_pair_align' format='txt' label='Tag Pair Alignments'>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
197 <filter>pair == '-pair' and paired_reads == 'true' and no != '-no'</filter>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
198 </data>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
199 <data name='trim_status' format='tabular' label='Trim Status'/>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
200
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
201 </outputs>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
202 <help>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
203
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
204 **What it does**
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
205
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
206 Assemble (Roche/454) reads using Newbler.
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
207
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
208 Download the manual here: http://galaxy.jgi-psf.org/static/manuals/GSFLXSystemSoftwareManual_PartC_Assembler-Mapper-SFFTools.pdf
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
209
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
210 .. class:: warningmark
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
211
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
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.
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
213
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
214 </help>
f036c7107601 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
parents:
diff changeset
215 </tool>