annotate tophat_wrapper.xml @ 2:8afd8a379d5f draft

planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Tue, 21 Jul 2015 16:01:00 -0400
parents 6eaefb5f755a
children 2ad64c5bb5f4
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
1 <tool id="tophat" name="Tophat for Illumina" version="1.5.0">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
2 <!-- Wrapper compatible with Tophat versions 1.3.0 to 1.4.1 -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
3 <description>Find splice junctions using RNA-seq data</description>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
4 <version_command>tophat --version</version_command>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
5 <requirements>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
6 <requirement type="package" version="0.1.18">samtools</requirement>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
7 <requirement type="package" version="0.12.7">bowtie</requirement>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
8 <requirement type="package" version="1.4.0">tophat</requirement>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
9 </requirements>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
10 <command interpreter="python">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
11 tophat_wrapper.py
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
12 ## Change this to accommodate the number of threads you have available.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
13 --num-threads="\${GALAXY_SLOTS:-4}"
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
14 ## Provide outputs.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
15 --junctions-output=$junctions
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
16 --hits-output=$accepted_hits
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
17
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
18 ## Handle reference file.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
19 #if $refGenomeSource.genomeSource == "history":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
20 --own-file=$refGenomeSource.ownFile
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
21 #else:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
22 --indexes-path="${refGenomeSource.index.fields.path}"
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
23 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
24
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
25 ## Are reads single-end or paired?
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
26 --single-paired=$singlePaired.sPaired
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
27
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
28 ## First input file always required.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
29 --input1=$input1
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
30
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
31 ## Set params based on whether reads are single-end or paired.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
32 #if $singlePaired.sPaired == "single":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
33 --settings=$singlePaired.sParams.sSettingsType
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
34 #if $singlePaired.sParams.sSettingsType == "full":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
35 -a $singlePaired.sParams.anchor_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
36 -m $singlePaired.sParams.splice_mismatches
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
37 -i $singlePaired.sParams.min_intron_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
38 -I $singlePaired.sParams.max_intron_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
39 -g $singlePaired.sParams.max_multihits
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
40 --min-segment-intron $singlePaired.sParams.min_segment_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
41 --max-segment-intron $singlePaired.sParams.max_segment_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
42 --initial-read-mismatches=$singlePaired.sParams.initial_read_mismatches
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
43 --seg-mismatches=$singlePaired.sParams.seg_mismatches
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
44 --seg-length=$singlePaired.sParams.seg_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
45 --library-type=$singlePaired.sParams.library_type
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
46
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
47 ## Indel search.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
48 #if $singlePaired.sParams.indel_search.allow_indel_search == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
49 ## --allow-indels
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
50 --max-insertion-length $singlePaired.sParams.indel_search.max_insertion_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
51 --max-deletion-length $singlePaired.sParams.indel_search.max_deletion_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
52 #else:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
53 --no-novel-indels
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
54 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
55
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
56 ## Supplying junctions parameters.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
57 #if $singlePaired.sParams.own_junctions.use_junctions == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
58 #if $singlePaired.sParams.own_junctions.gene_model_ann.use_annotations == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
59 -G $singlePaired.sParams.own_junctions.gene_model_ann.gene_annotation_model
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
60 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
61 #if $singlePaired.sParams.own_junctions.raw_juncs.use_juncs == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
62 -j $singlePaired.sParams.own_junctions.raw_juncs.raw_juncs
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
63 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
64 ## TODO: No idea why a string cast is necessary, but it is:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
65 #if str($singlePaired.sParams.own_junctions.no_novel_juncs) == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
66 --no-novel-juncs
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
67 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
68 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
69
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
70 #if $singlePaired.sParams.closure_search.use_search == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
71 --closure-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
72 --min-closure-exon $singlePaired.sParams.closure_search.min_closure_exon
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
73 --min-closure-intron $singlePaired.sParams.closure_search.min_closure_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
74 --max-closure-intron $singlePaired.sParams.closure_search.max_closure_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
75 #else:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
76 --no-closure-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
77 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
78 #if $singlePaired.sParams.coverage_search.use_search == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
79 --coverage-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
80 --min-coverage-intron $singlePaired.sParams.coverage_search.min_coverage_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
81 --max-coverage-intron $singlePaired.sParams.coverage_search.max_coverage_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
82 #else:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
83 --no-coverage-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
84 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
85 ## TODO: No idea why the type conversion is necessary, but it seems to be.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
86 #if str($singlePaired.sParams.microexon_search) == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
87 --microexon-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
88 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
89 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
90 #else:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
91 --input2=$singlePaired.input2
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
92 -r $singlePaired.mate_inner_distance
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
93 --settings=$singlePaired.pParams.pSettingsType
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
94 #if $singlePaired.pParams.pSettingsType == "full":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
95 --mate-std-dev=$singlePaired.pParams.mate_std_dev
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
96 -a $singlePaired.pParams.anchor_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
97 -m $singlePaired.pParams.splice_mismatches
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
98 -i $singlePaired.pParams.min_intron_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
99 -I $singlePaired.pParams.max_intron_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
100 -g $singlePaired.pParams.max_multihits
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
101 --min-segment-intron $singlePaired.pParams.min_segment_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
102 --max-segment-intron $singlePaired.pParams.max_segment_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
103 --initial-read-mismatches=$singlePaired.pParams.initial_read_mismatches
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
104 --seg-mismatches=$singlePaired.pParams.seg_mismatches
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
105 --seg-length=$singlePaired.pParams.seg_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
106 --library-type=$singlePaired.pParams.library_type
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
107
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
108 ## Indel search.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
109 #if $singlePaired.pParams.indel_search.allow_indel_search == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
110 ## --allow-indels
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
111 --max-insertion-length $singlePaired.pParams.indel_search.max_insertion_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
112 --max-deletion-length $singlePaired.pParams.indel_search.max_deletion_length
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
113 #else:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
114 --no-novel-indels
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
115 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
116
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
117 ## Supplying junctions parameters.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
118 #if $singlePaired.pParams.own_junctions.use_junctions == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
119 #if $singlePaired.pParams.own_junctions.gene_model_ann.use_annotations == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
120 -G $singlePaired.pParams.own_junctions.gene_model_ann.gene_annotation_model
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
121 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
122 #if $singlePaired.pParams.own_junctions.raw_juncs.use_juncs == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
123 -j $singlePaired.pParams.own_junctions.raw_juncs.raw_juncs
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
124 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
125 ## TODO: No idea why type cast is necessary, but it is:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
126 #if str($singlePaired.pParams.own_junctions.no_novel_juncs) == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
127 --no-novel-juncs
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
128 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
129 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
130
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
131 #if $singlePaired.pParams.closure_search.use_search == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
132 --closure-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
133 --min-closure-exon $singlePaired.pParams.closure_search.min_closure_exon
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
134 --min-closure-intron $singlePaired.pParams.closure_search.min_closure_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
135 --max-closure-intron $singlePaired.pParams.closure_search.max_closure_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
136 #else:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
137 --no-closure-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
138 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
139 #if $singlePaired.pParams.coverage_search.use_search == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
140 --coverage-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
141 --min-coverage-intron $singlePaired.pParams.coverage_search.min_coverage_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
142 --max-coverage-intron $singlePaired.pParams.coverage_search.max_coverage_intron
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
143 #else:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
144 --no-coverage-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
145 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
146 ## TODO: No idea why the type conversion is necessary, but it seems to be.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
147 #if str ($singlePaired.pParams.microexon_search) == "Yes":
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
148 --microexon-search
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
149 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
150 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
151 #end if
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
152 </command>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
153 <inputs>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
154 <param format="fastqsanger" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
155 <expand macro="refGenomeSourceConditional">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
156 <options from_data_table="tophat_indexes">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
157 <filter type="sort_by" column="2"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
158 <validator type="no_options" message="No genomes are available for the selected input dataset"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
159 </options>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
160 </expand>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
161 <conditional name="singlePaired">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
162 <param name="sPaired" type="select" label="Is this library mate-paired?">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
163 <option value="single">Single-end</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
164 <option value="paired">Paired-end</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
165 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
166 <when value="single">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
167 <conditional name="sParams">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
168 <param name="sSettingsType" type="select" label="TopHat settings to use" help="Use the Full parameter list to change default settings.">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
169 <option value="preSet">Default settings</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
170 <option value="full">Full parameter list</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
171 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
172 <when value="preSet" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
173 <!-- Full/advanced params. -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
174 <when value="full">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
175 <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
176 <option value="fr-unstranded">FR Unstranded</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
177 <option value="fr-firststrand">FR First Strand</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
178 <option value="fr-secondstrand">FR Second Strand</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
179 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
180 <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
181 <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
182 <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
183 <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
184 <conditional name="indel_search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
185 <param name="allow_indel_search" type="select" label="Allow indel search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
186 <option value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
187 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
188 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
189 <when value="No"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
190 <when value="Yes">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
191 <param name="max_insertion_length" type="integer" value="3" label="Max insertion length." help="The maximum insertion length." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
192 <param name="max_deletion_length" type="integer" value="3" label="Max deletion length." help="The maximum deletion length." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
193 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
194 </conditional>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
195 alignments (number of reads divided by average depth of coverage)" help="0.0 to 1.0 (0 to turn off)" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
196 <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
197 <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
198 <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
199 <param name="initial_read_mismatches" type="integer" min="0" value="2" label="Number of mismatches allowed in the initial read mapping" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
200 <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
201 <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
202
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
203 <!-- Options for supplying own junctions. -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
204 <conditional name="own_junctions">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
205 <param name="use_junctions" type="select" label="Use Own Junctions">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
206 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
207 <option value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
208 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
209 <when value="Yes">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
210 <conditional name="gene_model_ann">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
211 <param name="use_annotations" type="select" label="Use Gene Annotation Model">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
212 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
213 <option value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
214 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
215 <when value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
216 <when value="Yes">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
217 <param format="gtf,gff3" name="gene_annotation_model" type="data" label="Gene Model Annotations" help="TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping."/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
218 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
219 </conditional>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
220 <conditional name="raw_juncs">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
221 <param name="use_juncs" type="select" label="Use Raw Junctions">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
222 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
223 <option value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
224 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
225 <when value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
226 <when value="Yes">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
227 <param format="interval" name="raw_juncs" type="data" label="Raw Junctions" help="Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-] left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive."/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
228 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
229 </conditional>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
230 <param name="no_novel_juncs" type="select" label="Only look for supplied junctions">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
231 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
232 <option value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
233 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
234 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
235 <when value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
236 </conditional> <!-- /own_junctions -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
237
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
238 <!-- Closure search. -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
239 <conditional name="closure_search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
240 <param name="use_search" type="select" label="Use Closure Search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
241 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
242 <option value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
243 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
244 <when value="Yes">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
245 <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
246 <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
247 <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
248 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
249 <when value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
250 </conditional>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
251 <!-- Coverage search. -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
252 <conditional name="coverage_search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
253 <param name="use_search" type="select" label="Use Coverage Search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
254 <option selected="true" value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
255 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
256 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
257 <when value="Yes">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
258 <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
259 <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
260 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
261 <when value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
262 </conditional>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
263 <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
264 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
265 <option value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
266 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
267 </when> <!-- full -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
268 </conditional> <!-- sParams -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
269 </when> <!-- single -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
270 <when value="paired">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
271 <param format="fastqsanger" name="input2" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
272 <param name="mate_inner_distance" type="integer" value="20" label="Mean Inner Distance between Mate Pairs" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
273 <conditional name="pParams">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
274 <param name="pSettingsType" type="select" label="TopHat settings to use" help="Use the Full parameter list to change default settings.">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
275 <option value="preSet">Default settings</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
276 <option value="full">Full parameter list</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
277 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
278 <when value="preSet" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
279 <!-- Full/advanced params. -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
280 <when value="full">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
281 <param name="library_type" type="select" label="Library Type" help="TopHat will treat the reads as strand specific. Every read alignment will have an XS attribute tag. Consider supplying library type options below to select the correct RNA-seq protocol.">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
282 <option value="fr-unstranded">FR Unstranded</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
283 <option value="fr-firststrand">FR First Strand</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
284 <option value="fr-secondstrand">FR Second Strand</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
285 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
286 <param name="mate_std_dev" type="integer" value="20" label="Std. Dev for Distance between Mate Pairs" help="The standard deviation for the distribution on inner distances between mate pairs."/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
287 <param name="anchor_length" type="integer" value="8" label="Anchor length (at least 3)" help="Report junctions spanned by reads with at least this many bases on each side of the junction." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
288 <param name="splice_mismatches" type="integer" value="0" label="Maximum number of mismatches that can appear in the anchor region of spliced alignment" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
289 <param name="min_intron_length" type="integer" value="70" label="The minimum intron length" help="TopHat will ignore donor/acceptor pairs closer than this many bases apart." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
290 <param name="max_intron_length" type="integer" value="500000" label="The maximum intron length" help="When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
291 <expand macro="indel_searchConditional" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
292 <param name="max_multihits" type="integer" value="20" label="Maximum number of alignments to be allowed" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
293 <param name="min_segment_intron" type="integer" value="50" label="Minimum intron length that may be found during split-segment (default) search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
294 <param name="max_segment_intron" type="integer" value="500000" label="Maximum intron length that may be found during split-segment (default) search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
295 <param name="initial_read_mismatches" type="integer" min="0" value="2" label="Number of mismatches allowed in the initial read mapping" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
296 <param name="seg_mismatches" type="integer" min="0" max="3" value="2" label="Number of mismatches allowed in each segment alignment for reads mapped independently" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
297 <param name="seg_length" type="integer" value="25" label="Minimum length of read segments" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
298 <!-- Options for supplying own junctions. -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
299 <expand macro="own_junctionsConditional" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
300 <!-- Closure search. -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
301 <conditional name="closure_search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
302 <param name="use_search" type="select" label="Use Closure Search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
303 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
304 <option value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
305 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
306 <when value="Yes">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
307 <param name="min_closure_exon" type="integer" value="50" label="During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50." />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
308 <param name="min_closure_intron" type="integer" value="50" label="Minimum intron length that may be found during closure search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
309 <param name="max_closure_intron" type="integer" value="5000" label="Maximum intron length that may be found during closure search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
310 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
311 <when value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
312 </conditional>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
313 <!-- Coverage search. -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
314 <conditional name="coverage_search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
315 <param name="use_search" type="select" label="Use Coverage Search">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
316 <option selected="true" value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
317 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
318 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
319 <when value="Yes">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
320 <param name="min_coverage_intron" type="integer" value="50" label="Minimum intron length that may be found during coverage search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
321 <param name="max_coverage_intron" type="integer" value="20000" label="Maximum intron length that may be found during coverage search" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
322 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
323 <when value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
324 </conditional>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
325 <param name="microexon_search" type="select" label="Use Microexon Search" help="With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
326 <option value="No">No</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
327 <option value="Yes">Yes</option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
328 </param>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
329 </when> <!-- full -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
330 </conditional> <!-- pParams -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
331 </when> <!-- paired -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
332 </conditional>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
333 </inputs>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
334
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
335 <outputs>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
336 <data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
337 <expand macro="dbKeyActions" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
338 </data>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
339 <data format="bed" name="deletions" label="${tool.name} on ${on_string}: deletions" from_work_dir="tophat_out/deletions.bed">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
340 <expand macro="dbKeyActions" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
341 </data>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
342 <data format="bed" name="junctions" label="${tool.name} on ${on_string}: splice junctions" from_work_dir="tophat_out/junctions.bed">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
343 <expand macro="dbKeyActions" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
344 </data>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
345 <data format="bam" name="accepted_hits" label="${tool.name} on ${on_string}: accepted_hits" from_work_dir="tophat_out/accepted_hits.bam">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
346 <expand macro="dbKeyActions" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
347 </data>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
348 </outputs>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
349 <macros>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
350 <import>tophat_macros.xml</import>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
351 <macro name="dbKeyActions">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
352 <actions>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
353 <conditional name="refGenomeSource.genomeSource">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
354 <when value="indexed">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
355 <action type="metadata" name="dbkey">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
356 <option type="from_data_table" name="tophat_indexes" column="1" offset="0">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
357 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
358 <filter type="param_value" ref="refGenomeSource.index" column="0"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
359 </option>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
360 </action>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
361 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
362 <when value="history">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
363 <action type="metadata" name="dbkey">
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
364 <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
365 </action>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
366 </when>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
367 </conditional>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
368 </actions>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
369 </macro>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
370 </macros>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
371 <tests>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
372 <!-- Test base-space single-end reads with pre-built index and preset parameters -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
373 <test>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
374 <!-- TopHat commands:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
375 tophat -o tmp_dir -p 1 tophat_in1 test-data/tophat_in2.fastqsanger
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
376 Rename the files in tmp_dir appropriately
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
377 -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
378 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
379 <param name="genomeSource" value="indexed" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
380 <param name="index" value="tophat_test" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
381 <param name="sPaired" value="single" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
382 <param name="sSettingsType" value="preSet" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
383 <output name="junctions" file="tophat_out1j.bed" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
384 <output name="accepted_hits" file="tophat_out1h.bam" compare="sim_size" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
385 </test>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
386 <!-- Test using base-space test data: paired-end reads, index from history. -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
387 <test>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
388 <!-- TopHat commands:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
389 bowtie-build -f test-data/tophat_in1.fasta tophat_in1
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
390 tophat -o tmp_dir -p 1 -r 20 tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
391 Rename the files in tmp_dir appropriately
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
392 -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
393 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
394 <param name="genomeSource" value="history" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
395 <param name="ownFile" ftype="fasta" value="tophat_in1.fasta" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
396 <param name="sPaired" value="paired" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
397 <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
398 <param name="mate_inner_distance" value="20" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
399 <param name="pSettingsType" value="preSet" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
400 <output name="junctions" file="tophat_out2j.bed" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
401 <output name="accepted_hits" file="tophat_out2h.bam" compare="sim_size" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
402 </test>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
403 <!-- Test base-space single-end reads with user-supplied reference fasta and full parameters -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
404 <test>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
405 <!-- Tophat commands:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
406 bowtie-build -f test-data/tophat_in1.fasta tophat_in1
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
407 tophat -o tmp_dir -p 1 -a 8 -m 0 -i 70 -I 500000 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +closure-search +min-closure-exon 50 +min-closure-intron 50 +max-closure-intro 5000 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
408 Replace the + with double-dash
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
409 Rename the files in tmp_dir appropriately
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
410 -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
411 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
412 <param name="genomeSource" value="history"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
413 <param name="ownFile" value="tophat_in1.fasta"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
414 <param name="sPaired" value="single"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
415 <param name="sSettingsType" value="full"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
416 <param name="library_type" value="FR Unstranded"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
417 <param name="anchor_length" value="8"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
418 <param name="splice_mismatches" value="0"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
419 <param name="min_intron_length" value="70"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
420 <param name="max_intron_length" value="500000"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
421 <param name="max_multihits" value="40"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
422 <param name="min_segment_intron" value="50" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
423 <param name="max_segment_intron" value="500000" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
424 <param name="seg_mismatches" value="2"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
425 <param name="seg_length" value="25"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
426 <param name="allow_indel_search" value="Yes"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
427 <param name="max_insertion_length" value="3"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
428 <param name="max_deletion_length" value="3"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
429 <param name="use_junctions" value="Yes" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
430 <param name="use_annotations" value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
431 <param name="use_juncs" value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
432 <param name="no_novel_juncs" value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
433 <param name="use_search" value="Yes" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
434 <param name="min_closure_exon" value="50" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
435 <param name="min_closure_intron" value="50" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
436 <param name="max_closure_intron" value="5000" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
437 <param name="use_search" value="Yes" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
438 <param name="min_coverage_intron" value="50" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
439 <param name="max_coverage_intron" value="20000" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
440 <param name="microexon_search" value="Yes" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
441 <output name="insertions" file="tophat_out3i.bed" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
442 <output name="deletions" file="tophat_out3d.bed" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
443 <output name="junctions" file="tophat_out3j.bed" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
444 <output name="accepted_hits" file="tophat_out3h.bam" compare="sim_size" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
445 </test>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
446 <!-- Test base-space paired-end reads with user-supplied reference fasta and full parameters -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
447 <test>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
448 <!-- TopHat commands:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
449 tophat -o tmp_dir -r 20 -p 1 -a 8 -m 0 -i 70 -I 500000 -g 40 +coverage-search +min-coverage-intron 50 +max-coverage-intro 20000 +segment-mismatches 2 +segment-length 25 +microexon-search tophat_in1 test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
450 Replace the + with double-dash
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
451 Rename the files in tmp_dir appropriately
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
452 -->
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
453 <param name="input1" ftype="fastqsanger" value="tophat_in2.fastqsanger"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
454 <param name="genomeSource" value="indexed"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
455 <param name="index" value="tophat_test"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
456 <param name="sPaired" value="paired"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
457 <param name="input2" ftype="fastqsanger" value="tophat_in3.fastqsanger"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
458 <param name="mate_inner_distance" value="20"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
459 <param name="pSettingsType" value="full"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
460 <param name="library_type" value="FR Unstranded"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
461 <param name="mate_std_dev" value="20"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
462 <param name="anchor_length" value="8"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
463 <param name="splice_mismatches" value="0"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
464 <param name="min_intron_length" value="70"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
465 <param name="max_intron_length" value="500000"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
466 <param name="max_multihits" value="40"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
467 <param name="min_segment_intron" value="50" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
468 <param name="max_segment_intron" value="500000" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
469 <param name="seg_mismatches" value="2"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
470 <param name="seg_length" value="25"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
471 <param name="allow_indel_search" value="No"/>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
472 <param name="use_junctions" value="Yes" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
473 <param name="use_annotations" value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
474 <param name="use_juncs" value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
475 <param name="no_novel_juncs" value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
476 <param name="use_search" value="No" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
477 <param name="microexon_search" value="Yes" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
478 <output name="junctions" file="tophat_out4j.bed" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
479 <output name="accepted_hits" file="tophat_out4h.bam" compare="sim_size" />
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
480 </test>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
481 </tests>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
482
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
483 <help>
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
484 **Tophat Overview**
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
485
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
486 TopHat_ is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Please cite: Trapnell, C., Pachter, L. and Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
487
1
6eaefb5f755a Update Tophat URLs in help text.
Nate Coraor <nate@bx.psu.edu>
parents: 0
diff changeset
488 .. _Tophat: http://ccb.jhu.edu/software/tophat/
0
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
489
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
490 ------
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
491
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
492 **Know what you are doing**
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
493
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
494 .. class:: warningmark
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
495
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
496 There is no such thing (yet) as an automated gearshift in splice junction identification. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
497
1
6eaefb5f755a Update Tophat URLs in help text.
Nate Coraor <nate@bx.psu.edu>
parents: 0
diff changeset
498 .. __: http://ccb.jhu.edu/software/tophat/manual.shtml
0
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
499
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
500 ------
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
501
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
502 **Input formats**
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
503
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
504 Tophat accepts files in Sanger FASTQ format. Use the FASTQ Groomer to prepare your files.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
505
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
506 ------
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
507
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
508 **Outputs**
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
509
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
510 Tophat produces two output files:
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
511
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
512 - junctions -- A UCSC BED_ track of junctions reported by TopHat. Each junction consists of two connected BED blocks, where each block is as long as the maximal overhang of any read spanning the junction. The score is the number of alignments spanning the junction.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
513 - accepted_hits -- A list of read alignments in BAM_ format.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
514
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
515 .. _BED: http://genome.ucsc.edu/FAQ/FAQformat.html#format1
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
516 .. _BAM: http://samtools.sourceforge.net/
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
517
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
518 Two other possible outputs, depending on the options you choose, are insertions and deletions, both of which are in BED format.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
519
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
520 -------
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
521
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
522 **Tophat settings**
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
523
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
524 All of the options have a default value. You can change any of them. Some of the options in Tophat have been implemented here.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
525
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
526 ------
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
527
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
528 **Tophat parameter list**
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
529
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
530 This is a list of implemented Tophat options::
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
531
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
532 -r This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
533 selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
534 is required for paired end runs.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
535 --mate-std-dev INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
536 -a/--min-anchor-length INT The "anchor length". TopHat will report junctions spanned by reads with at least this many bases on each side of the junction. Note that individual spliced
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
537 alignments may span a junction with fewer than this many bases on one side. However, every junction involved in spliced alignments is supported by at least one
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
538 read with this many bases on each side. This must be at least 3 and the default is 8.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
539 -m/--splice-mismatches INT The maximum number of mismatches that may appear in the "anchor" region of a spliced alignment. The default is 0.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
540 -i/--min-intron-length INT The minimum intron length. TopHat will ignore donor/acceptor pairs closer than this many bases apart. The default is 70.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
541 -I/--max-intron-length INT The maximum intron length. When searching for junctions ab initio, TopHat will ignore donor/acceptor pairs farther than this many bases apart, except when such a pair is supported by a split segment alignment of a long read. The default is 500000.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
542 -g/--max-multihits INT Instructs TopHat to allow up to this many alignments to the reference for a given read, and suppresses all alignments for reads with more than this many
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
543 alignments. The default is 40.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
544 -G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
545 -j/--raw-juncs [juncs file] Supply TopHat with a list of raw junctions. Junctions are specified one per line, in a tab-delimited format. Records look like: [chrom] [left] [right] [+/-], left and right are zero-based coordinates, and specify the last character of the left sequenced to be spliced to the first character of the right sequence, inclusive.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
546 -no-novel-juncs Only look for junctions indicated in the supplied GFF file. (ignored without -G)
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
547 --no-closure-search Disables the mate pair closure-based search for junctions. Currently, has no effect - closure search is off by default.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
548 --closure-search Enables the mate pair closure-based search for junctions. Closure-based search should only be used when the expected inner distance between mates is small (about or less than 50bp)
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
549 --no-coverage-search Disables the coverage based search for junctions.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
550 --coverage-search Enables the coverage based search for junctions. Use when coverage search is disabled by default (such as for reads 75bp or longer), for maximum sensitivity.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
551 --microexon-search With this option, the pipeline will attempt to find alignments incident to microexons. Works only for reads 50bp or longer.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
552 --butterfly-search TopHat will use a slower but potentially more sensitive algorithm to find junctions in addition to its standard search. Consider using this if you expect that your experiment produced a lot of reads from pre-mRNA, that fall within the introns of your transcripts.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
553 --segment-mismatches Read segments are mapped independently, allowing up to this many mismatches in each segment alignment. The default is 2.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
554 --segment-length Each read is cut up into segments, each at least this long. These segments are mapped independently. The default is 25.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
555 --min-closure-exon During closure search for paired end reads, exonic hops in the potential splice graph must be at least this long. The default is 50.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
556 --min-closure-intron The minimum intron length that may be found during closure search. The default is 50.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
557 --max-closure-intron The maximum intron length that may be found during closure search. The default is 5000.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
558 --min-coverage-intron The minimum intron length that may be found during coverage search. The default is 50.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
559 --max-coverage-intron The maximum intron length that may be found during coverage search. The default is 20000.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
560 --min-segment-intron The minimum intron length that may be found during split-segment search. The default is 50.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
561 --max-segment-intron The maximum intron length that may be found during split-segment search. The default is 500000.
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
562 </help>
2
8afd8a379d5f planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 1
diff changeset
563 <citations>
8afd8a379d5f planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 1
diff changeset
564 <citation type="doi">10.1093/bioinformatics/btp120</citation>
8afd8a379d5f planemo upload commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
devteam
parents: 1
diff changeset
565 </citations>
0
1030acbecce6 Imported from capsule None
devteam
parents:
diff changeset
566 </tool>