Mercurial > repos > brasset_jensen > srnapipe

comparison sRNAPipe.xml @ 61:9185ca0a7b43 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated package according to recommendations.
author pierre.pouchin
date Wed, 16 Jan 2019 08:18:13 -0500
parents 9645d995fb3c
children e6c4f3e96e47
comparison
equal deleted inserted replaced
60:9645d995fb3c 61:9185ca0a7b43
1 <tool id="sRNAPipe" name="sRNAPipe" version="1.0"> 1 <tool id="sRNAPipe" name="sRNAPipe" version="1.1">
2 <description>In-depth study of small RNA</description> 2 <description>In-depth study of small RNA</description>
3 <command><![CDATA[ 3 <macros>
4 perl '$__tool_directory__/bin/sRNAPipe.pl' 4 <xml name="source">
5 5 <conditional name="source">
6 --fastq '${first_input}' 6 <param name="source" type="select" label="Will you select the database from your history or use a built-in index?">
7 --fastq_n '${first_input.name}' 7 <option value="indexed">Use a built-in index</option>
8 #for $input_file in $input_files: 8 <option value="history">Use one from the history</option>
9 --fastq '${input_file.additional_input}' 9 </param>
10 --fastq_n '${input_file.additional_input.name}' 10 <when value="indexed">
11 #end for 11 <param name="indices" argument="@ARG@" type="select" label="Select a reference genome" help="Also use @BUILD@">
12 12 <options from_data_table="bwa_indexes">
13 #if $Genome.refGenomeSource == "history": 13 <filter type="sort_by" column="2" />
14 --ref '${Genome.ownFile}' 14 <validator type="no_options" message="No indexes are available" />
15 --build_index 15 </options>
16 #else: 16 </param>
17 --ref '${Genome.indices.fields.path}' 17 </when>
18 #end if 18 <when value="history">
19 19 <param name="file" argument="@ARG@" type="data" format="fasta" label="Select a reference from history" />
20 #if $tRNAs.refGenomeSource == "history": 20 </when>
21 --tRNAs '${tRNAs.ownFile}' 21 </conditional>
22 --build_tRNAs 22 </xml>
23 #elif $tRNAs.refGenomeSource == "none": 23 </macros>
24 --tRNAs "None" 24 <requirements>
25 #else: 25 <requirement type="package" version="0.7.12">bwa</requirement>
26 --tRNAs '${tRNAs.indices.fields.path}' 26 <requirement type="package" version="2.24">bedtools</requirement>
27 #end if 27 <requirement type="package" version="1.5">samtools</requirement>
28 28 <requirement type="package" version="3.3.2">r-base</requirement>
29 #if $snRNAs.refGenomeSource == "history": 29 <requirement type="package" version="5.22.0">perl</requirement>
30 --snRNAs '${snRNAs.ownFile}' 30 <requirement type="package" version="2.50">perl-getopt-long</requirement>
31 --build_snRNAs 31 <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement>
32 #elif $snRNAs.refGenomeSource == "none": 32 <requirement type="package" version="0.34" >perl-statistics-r</requirement>
33 --snRNAs "None" 33 <requirement type="package" version="0.30">perl-string-random</requirement>
34 #else: 34 <requirement type="package" version="0.38" >perl-file-copy-recursive</requirement>
35 --snRNAs '${snRNAs.indices.fields.path}' 35 <requirement type="package" version="0.1" >perl-math-cdf</requirement>
36 #end if 36 <requirement type="package" version="3.6">r-plotrix</requirement>
37 37 <requirement type="package" version="1.14.0">bioconductor-sushi</requirement>
38 #if $rRNAs.refGenomeSource == "history": 38 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
39 --rRNAs "${rRNAs.ownFile}" 39 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
40 --build_rRNAs 40 </requirements>
41 #elif $rRNAs.refGenomeSource == "none": 41 <version_command>perl '$__tool_directory__/bin/sRNAPipe.pl'</version_command>
42 --rRNAs "None" 42 <command detect_errors="aggressive"><![CDATA[
43 #else: 43 perl '$__tool_directory__/bin/sRNAPipe.pl'
44 --rRNAs '${rRNAs.indices.fields.path}' 44
45 #end if 45 --fastq '${first_input}'
46 46 --fastq_n '${first_input.name}'
47 #if $miRNAs.refGenomeSource == "history": 47 #for $input_file in $input_files:
48 --miRNAs '${miRNAs.ownFile}' 48 --fastq '${input_file.additional_input}'
49 --build_miRNAs 49 --fastq_n '${input_file.additional_input.name}'
50 #else: 50 #end for
51 --miRNAs '${miRNAs.indices.fields.path}' 51
52 #end if 52 #if $genome.source.source == "history":
53 53 --ref '${genome.source.file}'
54 #if $transcripts.refGenomeSource == "history": 54 --build_index
55 --transcripts '${transcripts.ownFile}' 55 #else:
56 --build_transcripts 56 --ref '${genome.source.indices.fields.path}'
57 #else: 57 #end if
58 --transcripts '${transcripts.indices.fields.path}' 58
59 #end if 59 #if $tRNAs.source.source == "history":
60 60 --tRNAs '${tRNAs.source.file}'
61 #if $TE.refGenomeSource == "history": 61 --build_tRNAs
62 --TE '${TE.ownFile}' 62 #elif $tRNAs.source.source == "none":
63 --build_TE 63 --tRNAs "None"
64 #else: 64 #else:
65 --TE '${TE.indices.fields.path}' 65 --tRNAs '${tRNAs.source.indices.fields.path}'
66 #end if 66 #end if
67 67
68 --si_min $si_min 68 #if $snRNAs.source.source == "history":
69 --si_max $si_max 69 --snRNAs '${snRNAs.source.file}'
70 --pi_min $pi_min 70 --build_snRNAs
71 --pi_max $pi_max 71 #elif $snRNAs.source.source == "none":
72 --min $min 72 --snRNAs "None"
73 --max $max 73 #else:
74 74 --snRNAs '${snRNAs.source.indices.fields.path}'
75 --mis $mis 75 #end if
76 --misTE $misTE 76
77 --dir $html_out.files_path 77 #if $rRNAs.source.source == "history":
78 --html $html_out 78 --rRNAs '${rRNAs.source.file}'
79 --PPPon $PPPon 79 --build_rRNAs
80 ]]> 80 #elif $rRNAs.source.source == "none":
81 </command> 81 --rRNAs "None"
82 82 #else:
83 <requirements> 83 --rRNAs '${rRNAs.source.indices.fields.path}'
84 <requirement type="package" version="0.7.12">bwa</requirement> 84 #end if
85 <requirement type="package" version="2.24">bedtools</requirement> 85
86 <requirement type="package" version="1.5">samtools</requirement> 86 #if $miRNAs.source.source == "history":
87 <requirement type="package" version="3.3.2">r-base</requirement> 87 --miRNAs '${miRNAs.source.file}'
88 <requirement type="package" version="5.22.0">perl</requirement> 88 --build_miRNAs
89 <requirement type="package" version="2.50">perl-getopt-long</requirement> 89 #else:
90 <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement> 90 --miRNAs '${miRNAs.source.indices.fields.path}'
91 <requirement type="package" version="0.34" >perl-statistics-r</requirement> 91 #end if
92 <requirement type="package" version="0.30">perl-string-random</requirement> 92
93 <requirement type="package" version="0.38" >perl-file-copy-recursive</requirement> 93 #if $transcripts.source.source == "history":
94 <requirement type="package" version="0.1" >perl-math-cdf</requirement> 94 --transcripts '${transcripts.source.file}'
95 <requirement type="package" version="3.6">r-plotrix</requirement> 95 --build_transcripts
96 <requirement type="package" version="1.14.0">bioconductor-sushi</requirement> 96 #else:
97 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement> 97 --transcripts '${transcripts.source.indices.fields.path}'
98 <requirement type="package" version="2.2.1">r-ggplot2</requirement> 98 #end if
99 </requirements> 99
100 100 #if $TE.source.source == "history":
101 <inputs> 101 --TE '${TE.source.file}'
102 <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/> 102 --build_TE
103 <repeat name="input_files" title="Additional Fastq Files"> 103 #else:
104 <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/> 104 --TE '${TE.source.indices.fields.path}'
105 </repeat> 105 #end if
106 <conditional name="Genome"> 106
107 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> 107 --si_min $si_min
108 <option value="indexed">Use a built-in index</option> 108 --si_max $si_max
109 <option value="history">Use one from the history</option> 109 --pi_min $pi_min
110 </param> 110 --pi_max $pi_max
111 <when value="indexed"> 111 --min $min
112 <param name="indices" type="select" label="Select a reference genome"> 112 --max $max
113 <options from_data_table="bwa_indexes"> 113
114 <filter type="sort_by" column="2" /> 114 --mis $mis
115 <validator type="no_options" message="No indexes are available" /> 115 --misTE $misTE
116 </options> 116 --dir $html_out.files_path
117 </param> 117 --html $html_out
118 </when> 118 --PPPon $PPPon
119 <when value="history"> 119 ]]>
120 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> 120 </command>
121 </when> 121
122 </conditional> 122 <inputs>
123 <conditional name="transcripts"> 123 <param name="first_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name with --fastq_n"/>
124 <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?"> 124 <repeat name="input_files" title="Additional Fastq Files">
125 <option value="indexed">Use a built-in index</option> 125 <param name="additional_input" argument="--fastq" type="data" format="fastqsanger" label="fastqsanger (Q33)" help="Also set a name after each fastq with --fastq_n"/>
126 <option value="history">Use one from the history</option> 126 </repeat>
127 </param> 127 <section name="genome" title="Reference genome" expanded="true">
128 <when value="indexed"> 128 <expand macro="source" arg="--ref" build="--build_index"/>
129 <param name="indices" type="select" label="Select a transcripts reference"> 129 </section>
130 <options from_data_table="bwa_indexes"> 130 <section name="transcripts" title="Transcripts" expanded="true">
131 <filter type="sort_by" column="2" /> 131 <expand macro="source" arg="--transcripts" build="--build_transcripts"/>
132 <validator type="no_options" message="No indexes are available" /> 132 </section>
133 </options> 133 <section name="TE" title="Transposable Elements" expanded="true">
134 </param> 134 <expand macro="source" arg="--TE" build="--build_TE"/>
135 </when> 135 </section>
136 <when value="history"> 136 <section name="miRNAs" title="miRNAs" expanded="true">
137 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> 137 <expand macro="source" arg="--miRNAs" build="--build_miRNAs"/>
138 </when> 138 </section>
139 </conditional> 139 <section name="snRNAs" title="snRNAs" expanded="true">
140 <conditional name="TE"> 140 <expand macro="source" arg="--snRNAs" build="--build_snRNAs"/>
141 <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?"> 141 </section>
142 <option value="indexed">Use a built-in index</option> 142 <section name="rRNAs" title="rRNAs" expanded="true">
143 <option value="history">Use one from the history</option> 143 <expand macro="source" arg="--rRNAs" build="--build_rRNAs"/>
144 </param> 144 </section>
145 <when value="indexed"> 145 <section name="tRNAs" title="tRNAs" expanded="true">
146 <param name="indices" type="select" label="Select a TE reference"> 146 <expand macro="source" arg="--tRNAs" build="--build_tRNAs"/>
147 <options from_data_table="bwa_indexes"> 147 </section>
148 <filter type="sort_by" column="2" /> 148
149 <validator type="no_options" message="No indexes are available" /> 149 <param name="min" argument="--min" type="integer" value="18" label="minimum read size"/>
150 </options> 150 <param name="max" argument="--max" type="integer" value="29" label="maximum read size"/>
151 </param> 151 <param name="si_min" argument="--si_min" type="integer" value="21" label="lower bound of siRNA range"/>
152 </when> 152 <param name="si_max" argument="--si_max" type="integer" value="21" label="higher bound of siRNA range"/>
153 <when value="history"> 153 <param name="pi_min" argument="--pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
154 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> 154 <param name="pi_max" argument="--pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
155 </when> 155 <param name="mis" argument="--mis" type="integer" value="0" label="maximal genome mismatches"/>
156 </conditional> 156 <param name="misTE" argument="--misTE" type="integer" value="3" label="maximal TE mismatches"/>
157 <conditional name="miRNAs"> 157 <param name="PPPon" argument="--PPPon" type="boolean" checked="true" label="PPPartners"/>
158 <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?"> 158 </inputs>
159 <option value="indexed">Use a built-in index</option> 159 <outputs>
160 <option value="history">Use one from the history</option> 160 <data format="html" name="html_out" label="${tool.name} on ${first_input.name} (${on_string}): HTML report"/>
161 </param> 161 <collection type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
162 <when value="indexed"> 162 <discover_datasets format ="fastqsanger" pattern="__designation_and_ext__" directory="fastq_dir" />
163 <param name="indices" type="select" label="Select a miRNA reference">
164 <options from_data_table="bwa_indexes">
165 <filter type="sort_by" column="2" />
166 <validator type="no_options" message="No indexes are available" />
167 </options>
168 </param>
169 </when>
170 <when value="history">
171 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
172 </when>
173 </conditional>
174 <conditional name="snRNAs">
175 <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">
176 <option value="indexed">Use a built-in index</option>
177 <option value="history">Use one from the history</option>
178 <option value="none">None</option>
179 </param>
180 <when value="indexed">
181 <param name="indices" type="select" label="Select a snRNAs reference">
182 <options from_data_table="bwa_indexes">
183 <filter type="sort_by" column="2" />
184 <validator type="no_options" message="No indexes are available" />
185 </options>
186 </param>
187 </when>
188 <when value="history">
189 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
190 </when>
191 </conditional>
192 <conditional name="rRNAs">
193 <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">
194 <option value="indexed">Use a built-in index</option>
195 <option value="history">Use one from the history</option>
196 <option value="none">None</option>
197 </param>
198 <when value="indexed">
199 <param name="indices" type="select" label="Select a rRNAs reference">
200 <options from_data_table="bwa_indexes">
201 <filter type="sort_by" column="2" />
202 <validator type="no_options" message="No indexes are available" />
203 </options>
204 </param>
205 </when>
206 <when value="history">
207 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
208 </when>
209 </conditional>
210 <conditional name="tRNAs">
211 <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">
212 <option value="indexed">Use a built-in index</option>
213 <option value="history">Use one from the history</option>
214 <option value="none">None</option>
215 </param>
216 <when value="indexed">
217 <param name="indices" type="select" label="Select a tRNA reference">
218 <options from_data_table="bwa_indexes">
219 <filter type="sort_by" column="2" />
220 <validator type="no_options" message="No indexes are available" />
221 </options>
222 </param>
223 </when>
224 <when value="history">
225 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
226 </when>
227 </conditional>
228
229 <param name="min" type="integer" value="18" label="minimum read size"/>
230 <param name="max" type="integer" value="29" label="maximum read size"/>
231 <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/>
232 <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>
233 <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
234 <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
235
236 <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>
237 <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>
238 <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>
239 </inputs>
240 <outputs>
241 <data format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>
242
243 <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
244 <discover_datasets format ="fastqsanger" pattern="(?P&lt;name&gt;.*)" directory="fastq_dir" />
245 </collection> 163 </collection>
246 164 </outputs>
247 </outputs> 165 <tests>
248 <help> 166 <test>
167 <param name="first_input" value="reads-sample-small.fastq" />
168 <section name="genome">
169 <conditional name="source">
170 <param name="source" value="history" />
171 <param name="file" value ="genome-small.fa" />
172 </conditional>
173 </section>
174 <section name="transcripts">
175 <conditional name="source">
176 <param name="source" value="history" />
177 <param name="file" value ="transcripts-file-small.fa" />
178 </conditional>
179 </section>
180 <section name="TE">
181 <conditional name="source">
182 <param name="source" value="history" />
183 <param name="file" value ="TE-file-small.fa" />
184 </conditional>
185 </section>
186 <section name="miRNAs">
187 <conditional name="source">
188 <param name="source" value="history" />
189 <param name="file" value ="mirbase-21-dme-hairpins-16jul2015.fa" />
190 </conditional>
191 </section>
192 <section name="snRNAs">
193 <conditional name="source">
194 <param name="source" value="history" />
195 <param name="file" value ="dmel-all-sn-snoRNA-r6.03.fasta" />
196 </conditional>
197 </section>
198 <section name="rRNAs">
199 <conditional name="source">
200 <param name="source" value="history" />
201 <param name="file" value ="dmel-all-rRNA-r6.03.fasta" />
202 </conditional>
203 </section>
204 <section name="tRNAs">
205 <conditional name="source">
206 <param name="source" value="history" />
207 <param name="file" value ="dmel-all-tRNA-r6.03.fasta" />
208 </conditional>
209 </section>
210 <param name="min" value="18" />
211 <param name="max" value="29" />
212 <param name="si_min" value="21" />
213 <param name="si_max" value="21" />
214 <param name="pi_min" value="23" />
215 <param name="pi_max" value="29" />
216 <param name="mis" value="0" />
217 <param name="misTE" value="3" />
218 <param name="PPPon" value="true" />
219 <output name='html_out' file="res.html" compare='diff' lines_diff = '10'/>
220 <output_collection name="output_fastqsanger" type="list">
221 <element name="reads-sample-small.fastq_all_mappers" file="fastq_dir/reads-sample-small.fastq_all_mappers.fastq" />
222 <element name="reads-sample-small.fastq-bonafide_reads-genome" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome.fastq" />
223 <element name="reads-sample-small.fastq-bonafide_reads-genome_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-genome_uni.fastq" />
224 <element name="reads-sample-small.fastq-bonafide_reads-TEs" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs.fastq" />
225 <element name="reads-sample-small.fastq-bonafide_reads-TEs_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-TEs_uni.fastq" />
226 <element name="reads-sample-small.fastq-bonafide_reads-transcripts" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts.fastq" />
227 <element name="reads-sample-small.fastq-bonafide_reads-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-bonafide_reads-transcripts_uni.fastq" />
228 <element name="reads-sample-small.fastq-miRNAs-genome" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome.fastq" />
229 <element name="reads-sample-small.fastq-miRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-genome_uni.fastq" />
230 <element name="reads-sample-small.fastq-miRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-TEs_uni.fastq" />
231 <element name="reads-sample-small.fastq-miRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts.fastq" />
232 <element name="reads-sample-small.fastq-miRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-miRNAs-transcripts_uni.fastq" />
233 <element name="reads-sample-small.fastq-piRNAs-genome" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome.fastq" />
234 <element name="reads-sample-small.fastq-piRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-genome_uni.fastq" />
235 <element name="reads-sample-small.fastq-piRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs.fastq" />
236 <element name="reads-sample-small.fastq-piRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-TEs_uni.fastq" />
237 <element name="reads-sample-small.fastq-piRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts.fastq" />
238 <element name="reads-sample-small.fastq-piRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-piRNAs-transcripts_uni.fastq" />
239 <element name="reads-sample-small.fastq-siRNAs-genome" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome.fastq" />
240 <element name="reads-sample-small.fastq-siRNAs-genome_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-genome_uni.fastq" />
241 <element name="reads-sample-small.fastq-siRNAs-TEs" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs.fastq" />
242 <element name="reads-sample-small.fastq-siRNAs-TEs_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-TEs_uni.fastq" />
243 <element name="reads-sample-small.fastq-siRNAs-transcripts" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts.fastq" />
244 <element name="reads-sample-small.fastq-siRNAs-transcripts_uni" file="fastq_dir/reads-sample-small.fastq-siRNAs-transcripts_uni.fastq" />
245 <element name="reads-sample-small.fastq_unique_mappers" file="fastq_dir/reads-sample-small.fastq_unique_mappers.fastq" />
246 <element name="reads-sample-small.fastq_unmapped" file="fastq_dir/reads-sample-small.fastq_unmapped.fastq" />
247 </output_collection>
248 </test>
249 </tests>
250 <help>
249 **User manual** 251 **User manual**
250 "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf" 252 "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
251 </help> 253 </help>
254 <citations>
255 <citation type="doi">10.1038/nature12962</citation>
256 <citation type="doi">10.1038/nature11233</citation>
257 <citation type="doi">10.1186/gb4172</citation>
258 <citation type="doi">10.1038/nature04916</citation>
259 <citation type="doi">10.1016/j.cell.2007.01.043</citation>
260 <citation type="doi">10.1016/j.celrep.2015.02.062</citation>
261 <citation type="doi">10.1093/bioinformatics/btp324</citation>
262 <citation type="doi">10.1093/bioinformatics/btp352</citation>
263 <citation type="doi">10.1002/0471250953.bi1112s47</citation>
264 <citation type="doi">10.1093/bioinformatics/btu379</citation>
265 <citation type="doi">10.1002/embr.201337898</citation>
266 <citation type="doi">10.1038/ncomms13739</citation>
267 <citation type="doi">10.1093/nar/gkt310</citation>
268 <citation type="doi">10.1186/s13072-015-0041-5</citation>
269 <citation type="doi">10.1093/bioinformatics/btu647</citation>
270 </citations>
252 </tool> 271 </tool>