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comparison BSseeker2/galaxy/bs_seeker2_wrapper.xml @ 0:e6df770c0e58 draft

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Initial upload
author weilong-guo
date Fri, 12 Jul 2013 18:47:28 -0400
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1 <tool id="bs_seeker_wrapper" name="BS-Seeker2" version="2.0.0">
2 <requirements><requirement type='package'>bs_seeker2</requirement></requirements>
3 <description>Versatile aligner for bisulfite sequencing data</description>
4 <command interpreter="python">
5 bs_seeker2_wrapper.py
6 ### define exec path
7 ### --exec-path "/u/home/galaxy/galaxy/GalaxyTools/bin"
8 ### [Please change the following path to your local directory]
9 --exec-path "/Users/weilong/Documents/program/BSseeker2"
10 ### output
11 --align--output $align_output
12 --call_methylation--wig $call_methylation_wig
13 --call_methylation--CGmap $call_methylation_CGmap
14 --call_methylation--ATCGmap $call_methylation_ATCGmap
15 --call_methylation--txt
16
17 #if $singlePaired.sPaired == "paired"
18 --align--input_1 $input1
19 --align--input_2 $singlePaired.input2
20 #end if
21
22
23 ### aligner
24 --align--aligner ${choosealigner.aligner}
25
26 ### Index from history or built-in
27 #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history"
28 --build--file ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
29 --build--aligner ${choosealigner.aligner}
30 --align-g ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
31 --align--db ${choosealigner.rrbsFragments.refGenomeSource.ownFile}
32 #else if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "indexed"
33 --align--db ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}
34 --align-g ${choosealigner.rrbsFragments.refGenomeSource.index.fields.path}/${choosealigner.rrbsFragments.refGenomeSource.index.fields.dbkey}.fa
35
36 #end if
37
38 ### RRBS or WGBS
39 #if $choosealigner.rrbsFragments.Fragmented == "Yes"
40 #if $choosealigner.rrbsFragments.refGenomeSource.genomeSource == "history"
41 --build--rrbs
42 --build--low ${choosealigner.rrbsFragments.lowerBound}
43 --build--up ${choosealigner.rrbsFragments.upperBound}
44 #end if
45 --align--rrbs
46 --align--low ${choosealigner.rrbsFragments.lowerBound}
47 --align--up ${choosealigner.rrbsFragments.upperBound}
48 #end if
49
50
51
52 ### Inputs
53 #if $singlePaired.sPaired == "single"
54 --align-i $input1
55 #end if
56
57 ### Library type
58 --align-t $tag
59
60 ### other general options
61 #if $sParams.sSettingsType == "preSet"
62 --align--start_base 1
63 --align--end_base 200
64 --align--mis 4
65 #end if
66
67 ### adapter information
68 #if $adapterInfo.useAdapter == "Yes"
69 --align--adapter ${adapterInfo.adapter_file}
70 #end if
71
72 #if $sParams.sSettingsType == "full"
73 --align--start_base ${sParams.start_base}
74 --align--end_base ${sParams.end_base}
75 --align--mis ${sParams.num_mismatch}
76 #end if
77
78 </command>
79 <inputs>
80 <param format="fastq,fasta,qseq" name="input1" type="data" label="Input your read file" help="reads file in fastq, qseq or fasta format" />
81 <conditional name="singlePaired">
82 <param name="sPaired" type="select" label="Is this library mate-paired?">
83 <option value="single">Single-end</option>
84 <option value="paired">Paired-end</option>
85 </param>
86 <when value="paired">
87 <param format="fastq,fasta,qseq" name="input2" type="data" label="Input your read file 2" help="reads in fastq, qseq or fasta format" />
88 <param name="min_ins_distance" type="integer" value="-1" label=" Minimum insert size for valid paired-end alignments" />
89 <param name="max_ins_distance" type="integer" value="400" label="Maximum insert size for valid paired-end alignments" />
90 </when>
91 </conditional>
92 <param name="tag" type="select" label="Type of libraries">
93 <option value="N">directional libraries</option>
94 <option value="Y">undirectional libraries</option>
95 </param>
96 <conditional name="choosealigner">
97 <param name="aligner" type="select" label="Short reads aligner">
98 <option value="bowtie">bowtie</option>
99 <option value="bowtie2">bowtie2</option>
100 </param>
101 <when value="bowtie">
102 <conditional name="rrbsFragments">
103 <param name="Fragmented" type="select" label="RRBS-seq reads" help="">
104 <option value="No">No</option>
105 <option value="Yes">Yes</option>
106 </param>
107 <when value="Yes">
108 <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" />
109 <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" />
110 <conditional name="refGenomeSource">
111 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
112 <option value="indexed">Use a built-in index</option>
113 <option value="history">Use one from the history</option>
114 </param>
115 <when value="indexed">
116 <param name="index" type="select" label="Select a reference genome (RRBS, bowtie)">
117 <options from_data_table="bs_seeker2_indexes_RRBS_bowtie">
118 <filter type="sort_by" column="2"/>
119 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
120 </options>
121 </param>
122 </when>
123 <when value="history">
124 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
125 </when>
126 </conditional>
127 </when>
128 <when value="No">
129 <conditional name="refGenomeSource">
130 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
131 <option value="indexed">Use a built-in index</option>
132 <option value="history">Use one from the history</option>
133 </param>
134 <when value="indexed">
135 <param name="index" type="select" label="Select a reference genome (WGBS, bowtie)">
136 <options from_data_table="bs_seeker2_indexes_WGBS_bowtie">
137 <filter type="sort_by" column="2"/>
138 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
139 </options>
140 </param>
141 </when>
142 <when value="history">
143 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
144 </when>
145 </conditional>
146 </when>
147 </conditional>
148 </when>
149
150 <when value="bowtie2">
151 <conditional name="rrbsFragments">
152 <param name="Fragmented" type="select" label="RRBS-seq reads" help="">
153 <option value="No">No</option>
154 <option value="Yes">Yes</option>
155 </param>
156 <when value="Yes">
157 <param name="lowerBound" type="integer" value="40" label="The lower bound for RRBS fragments" help="Default: 40" />
158 <param name="upperBound" type="integer" value="500" label="The upper bound for RRBS fragments" help="Default: 500" />
159 <conditional name="refGenomeSource">
160 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
161 <option value="indexed">Use a built-in index</option>
162 <option value="history">Use one from the history</option>
163 </param>
164 <when value="indexed">
165 <param name="index" type="select" label="Select a reference genome (RRBS, bowtie2)">
166 <options from_data_table="bs_seeker2_indexes_RRBS_bowtie2">
167 <filter type="sort_by" column="2"/>
168 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
169 </options>
170 </param>
171 </when>
172 <when value="history">
173 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
174 </when>
175 </conditional>
176 </when>
177 <when value="No">
178 <conditional name="refGenomeSource">
179 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="">
180 <option value="indexed">Use a built-in index</option>
181 <option value="history">Use one from the history</option>
182 </param>
183 <when value="indexed">
184 <param name="index" type="select" label="Select a reference genome (WGBS, bowtie2)">
185 <options from_data_table="bs_seeker2_indexes_WGBS_bowtie2">
186 <filter type="sort_by" column="2"/>
187 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
188 </options>
189 </param>
190 </when>
191 <when value="history">
192 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
193 </when>
194 </conditional>
195 </when>
196 </conditional>
197 </when>
198 </conditional>
199 <conditional name="adapterInfo">
200 <param name="useAdapter" type="select" label="adapter sequence">
201 <option value="noAdapter">No</option>
202 <option value="withAdapter">Yes</option>
203 </param>
204 <when value="withAdapter">
205 <param format="txt" name="adapter_file" type="data" label="Input file of your adaptor sequences" help="Input text file of your adaptor sequences" />
206 </when>
207 </conditional>
208
209 <conditional name="sParams">
210 <param name="sSettingsType" type="select" label="BS Seeker2 settings to use" help="You can use the default settings or set customer values for the BS Seeker2 parameters.">
211 <option value="preSet">User Defaults</option>
212 <option value="full">Full parameter list</option>
213 </param>
214 <when value="preSet" />
215 <when value="full">
216 <param name="start_base" type="integer" value="1" label="The start base of the read to be mapped" help="" />
217 <param name="end_base" type="integer" value="200" label="The end base of the read to be mapped" help="" />
218
219 <param name="num_mismatch" type="integer" value="4" label="Number of mismatches" help="(INT) Default: 4" />
220 </when>
221 </conditional>
222
223 </inputs>
224
225 <outputs>
226 <data format="bam" name="align_output" label="BAM Alignments"> </data>
227 <data format="wig" name="call_methylation_wig" label="Methylation Levels"> </data>
228 <data format="tabular" name="call_methylation_CGmap" label="CGmap file"> </data>
229 <data format="tabular" name="call_methylation_ATCGmap" label="ATCGmap file"> </data>
230
231 </outputs>
232 <help>
233 **What it does**
234
235 BS-Seeker2 is a seamlessly pipeline for mapping bisulfite sequencing data and generating detailed DNA methylome. BS-Seeker2 improves mappability by using local alignment, and is tailored for RRBS library by building special index, with higher efficiency and accuracy. This is the Galaxy version of BS-Seeker2.
236
237 ------
238
239 **Resources**
240
241 The homepage for BS-Seeker2 is http://pellegrini.mcdb.ucla.edu/BS_Seeker2/.
242
243 For more information of BS-Seeker2, please refer to https://github.com/BSSeeker/BSseeker2.
244
245 ------
246
247 **Example**
248
249 - Adapter file::
250
251 AGATCGGAAGAGCACACGTC
252
253
254 </help>
255 </tool>