|
52
|
1 <tool id="sRNAPipe" name="sRNAPipe" version="0.0.1">
|
|
40
|
2 <description>In-depth study of small RNA</description>
|
|
|
3 <command interpreter="perl">
|
|
|
4
|
|
|
5 ./bin/sRNAPipe.pl
|
|
|
6
|
|
|
7 --fastq ${first_input}
|
|
|
8 --fastq_n ${first_input.name}
|
|
|
9 #for $input_file in $input_files:
|
|
|
10 --fastq ${input_file.additional_input}
|
|
|
11 --fastq_n ${input_file.additional_input.name}
|
|
|
12 #end for
|
|
|
13
|
|
|
14 #if $Genome.refGenomeSource == "history":
|
|
|
15 --ref "${Genome.ownFile}"
|
|
|
16 --build_index
|
|
|
17 #else:
|
|
|
18 --ref "${Genome.indices.fields.path}"
|
|
|
19 #end if
|
|
|
20
|
|
|
21 #if $tRNAs.refGenomeSource == "history":
|
|
|
22 --tRNAs "${tRNAs.ownFile}"
|
|
|
23 --build_tRNAs
|
|
|
24 #elif $tRNAs.refGenomeSource == "none":
|
|
|
25 --tRNAs "None"
|
|
|
26 #else:
|
|
|
27 --tRNAs "${tRNAs.indices.fields.path}"
|
|
|
28 #end if
|
|
|
29
|
|
|
30 #if $snRNAs.refGenomeSource == "history":
|
|
|
31 --snRNAs "${snRNAs.ownFile}"
|
|
|
32 --build_snRNAs
|
|
|
33 #elif $snRNAs.refGenomeSource == "none":
|
|
|
34 --snRNAs "None"
|
|
|
35 #else:
|
|
|
36 --snRNAs "${snRNAs.indices.fields.path}"
|
|
|
37 #end if
|
|
|
38
|
|
|
39 #if $rRNAs.refGenomeSource == "history":
|
|
|
40 --rRNAs "${rRNAs.ownFile}"
|
|
|
41 --build_rRNAs
|
|
|
42 #elif $rRNAs.refGenomeSource == "none":
|
|
|
43 --rRNAs "None"
|
|
|
44 #else:
|
|
|
45 --rRNAs "${rRNAs.indices.fields.path}"
|
|
|
46 #end if
|
|
|
47
|
|
|
48 #if $miRNAs.refGenomeSource == "history":
|
|
|
49 --miRNAs "${miRNAs.ownFile}"
|
|
|
50 --build_miRNAs
|
|
|
51 #else:
|
|
|
52 --miRNAs "${miRNAs.indices.fields.path}"
|
|
|
53 #end if
|
|
|
54
|
|
|
55 #if $transcripts.refGenomeSource == "history":
|
|
|
56 --transcripts "${transcripts.ownFile}"
|
|
|
57 --build_transcripts
|
|
|
58 #else:
|
|
|
59 --transcripts "${transcripts.indices.fields.path}"
|
|
|
60 #end if
|
|
|
61
|
|
|
62 #if $TE.refGenomeSource == "history":
|
|
|
63 --TE "${TE.ownFile}"
|
|
|
64 --build_TE
|
|
|
65 #else:
|
|
|
66 --TE "${TE.indices.fields.path}"
|
|
|
67 #end if
|
|
|
68
|
|
|
69 --si_min $si_min
|
|
|
70 --si_max $si_max
|
|
|
71 --pi_min $pi_min
|
|
|
72 --pi_max $pi_max
|
|
|
73 --min $min
|
|
|
74 --max $max
|
|
|
75
|
|
|
76 --mis $mis
|
|
|
77 --misTE $misTE
|
|
|
78 --dir $html_out.files_path
|
|
|
79 --html $html_out
|
|
|
80 --PPPon $PPPon
|
|
|
81 </command>
|
|
|
82
|
|
|
83 <requirements>
|
|
41
|
84 <requirement type="package" version="0.7.12">bwa</requirement>
|
|
|
85 <requirement type="package" version="2.24">bedtools</requirement>
|
|
|
86 <requirement type="package" version="1.2">samtools</requirement>
|
|
52
|
87 <requirement type="package" version="3.3.2">r-base</requirement>
|
|
|
88 <requirement type="package" version="5.20.3.1">perl</requirement>
|
|
|
89 <requirement type="package" version="2.50">perl-getopt-long</requirement>
|
|
53
|
90 <requirement type="package" version="1.17">perl-parallel-forkmanager</requirement>
|
|
52
|
91 <requirement type="package" version="0.34" >perl-statistics-r</requirement>
|
|
53
|
92 <requirement type="package" version="0.30">perl-string-random</requirement>
|
|
52
|
93 <requirement type="package" version="3.6">r-plotrix</requirement>
|
|
|
94 <requirement type="package" version="1.14.0">bioconductor-sushi</requirement>
|
|
53
|
95 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
|
|
|
96 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
|
|
40
|
97 </requirements>
|
|
|
98
|
|
|
99 <inputs>
|
|
|
100 <param format="fastqsanger" name="first_input" type="data" label="fastqsanger (Q33)" help=""/>
|
|
|
101 <repeat name="input_files" title="Additional Fastq Files">
|
|
|
102 <param format="fastqsanger" name="additional_input" type="data" label="fastqsanger (Q33)" help=""/>
|
|
|
103 </repeat>
|
|
|
104 <conditional name="Genome">
|
|
|
105 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
|
|
|
106 <option value="indexed">Use a built-in index</option>
|
|
|
107 <option value="history">Use one from the history</option>
|
|
|
108 </param>
|
|
|
109 <when value="indexed">
|
|
|
110 <param name="indices" type="select" label="Select a reference genome">
|
|
|
111 <options from_data_table="bwa_indexes">
|
|
|
112 <filter type="sort_by" column="2" />
|
|
|
113 <validator type="no_options" message="No indexes are available" />
|
|
|
114 </options>
|
|
|
115 </param>
|
|
|
116 </when>
|
|
|
117 <when value="history">
|
|
|
118 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
|
|
|
119 </when>
|
|
|
120 </conditional>
|
|
|
121 <conditional name="transcripts">
|
|
|
122 <param name="refGenomeSource" type="select" label="Will you select transcripts database from your history or use a built-in index?">
|
|
|
123 <option value="indexed">Use a built-in index</option>
|
|
|
124 <option value="history">Use one from the history</option>
|
|
|
125 </param>
|
|
|
126 <when value="indexed">
|
|
|
127 <param name="indices" type="select" label="Select a transcripts reference">
|
|
|
128 <options from_data_table="bwa_indexes">
|
|
|
129 <filter type="sort_by" column="2" />
|
|
|
130 <validator type="no_options" message="No indexes are available" />
|
|
|
131 </options>
|
|
|
132 </param>
|
|
|
133 </when>
|
|
|
134 <when value="history">
|
|
|
135 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
|
|
|
136 </when>
|
|
|
137 </conditional>
|
|
|
138 <conditional name="TE">
|
|
|
139 <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?">
|
|
|
140 <option value="indexed">Use a built-in index</option>
|
|
|
141 <option value="history">Use one from the history</option>
|
|
|
142 </param>
|
|
|
143 <when value="indexed">
|
|
|
144 <param name="indices" type="select" label="Select a TE reference">
|
|
|
145 <options from_data_table="bwa_indexes">
|
|
|
146 <filter type="sort_by" column="2" />
|
|
|
147 <validator type="no_options" message="No indexes are available" />
|
|
|
148 </options>
|
|
|
149 </param>
|
|
|
150 </when>
|
|
|
151 <when value="history">
|
|
|
152 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
|
|
|
153 </when>
|
|
|
154 </conditional>
|
|
|
155 <conditional name="miRNAs">
|
|
|
156 <param name="refGenomeSource" type="select" label="Will you select miRNA database from your history or use a built-in index?">
|
|
|
157 <option value="indexed">Use a built-in index</option>
|
|
|
158 <option value="history">Use one from the history</option>
|
|
|
159 </param>
|
|
|
160 <when value="indexed">
|
|
|
161 <param name="indices" type="select" label="Select a miRNA reference">
|
|
|
162 <options from_data_table="bwa_indexes">
|
|
|
163 <filter type="sort_by" column="2" />
|
|
|
164 <validator type="no_options" message="No indexes are available" />
|
|
|
165 </options>
|
|
|
166 </param>
|
|
|
167 </when>
|
|
|
168 <when value="history">
|
|
|
169 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
|
|
|
170 </when>
|
|
|
171 </conditional>
|
|
|
172 <conditional name="snRNAs">
|
|
|
173 <param name="refGenomeSource" type="select" label="Will you select snRNA database from your history or use a built-in index?">
|
|
|
174 <option value="indexed">Use a built-in index</option>
|
|
|
175 <option value="history">Use one from the history</option>
|
|
|
176 <option value="none">None</option>
|
|
|
177 </param>
|
|
|
178 <when value="indexed">
|
|
|
179 <param name="indices" type="select" label="Select a snRNAs reference">
|
|
|
180 <options from_data_table="bwa_indexes">
|
|
|
181 <filter type="sort_by" column="2" />
|
|
|
182 <validator type="no_options" message="No indexes are available" />
|
|
|
183 </options>
|
|
|
184 </param>
|
|
|
185 </when>
|
|
|
186 <when value="history">
|
|
|
187 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
|
|
|
188 </when>
|
|
|
189 </conditional>
|
|
|
190 <conditional name="rRNAs">
|
|
|
191 <param name="refGenomeSource" type="select" label="Will you select rRNAs database from your history or use a built-in index?">
|
|
|
192 <option value="indexed">Use a built-in index</option>
|
|
|
193 <option value="history">Use one from the history</option>
|
|
|
194 <option value="none">None</option>
|
|
|
195 </param>
|
|
|
196 <when value="indexed">
|
|
|
197 <param name="indices" type="select" label="Select a rRNAs reference">
|
|
|
198 <options from_data_table="bwa_indexes">
|
|
|
199 <filter type="sort_by" column="2" />
|
|
|
200 <validator type="no_options" message="No indexes are available" />
|
|
|
201 </options>
|
|
|
202 </param>
|
|
|
203 </when>
|
|
|
204 <when value="history">
|
|
|
205 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
|
|
|
206 </when>
|
|
|
207 </conditional>
|
|
|
208 <conditional name="tRNAs">
|
|
|
209 <param name="refGenomeSource" type="select" label="Will you select tRNA database from your history or use a built-in index?">
|
|
|
210 <option value="indexed">Use a built-in index</option>
|
|
|
211 <option value="history">Use one from the history</option>
|
|
|
212 <option value="none">None</option>
|
|
|
213 </param>
|
|
|
214 <when value="indexed">
|
|
|
215 <param name="indices" type="select" label="Select a tRNA reference">
|
|
|
216 <options from_data_table="bwa_indexes">
|
|
|
217 <filter type="sort_by" column="2" />
|
|
|
218 <validator type="no_options" message="No indexes are available" />
|
|
|
219 </options>
|
|
|
220 </param>
|
|
|
221 </when>
|
|
|
222 <when value="history">
|
|
|
223 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" />
|
|
|
224 </when>
|
|
|
225 </conditional>
|
|
|
226
|
|
|
227 <param name="min" type="integer" value="18" label="minimum read size"/>
|
|
|
228 <param name="max" type="integer" value="29" label="maximum read size"/>
|
|
|
229 <param name="si_min" type="integer" value="21" label="lower bound of siRNA range"/>
|
|
|
230 <param name="si_max" type="integer" value="21" label="higher bound of siRNA range"/>
|
|
|
231 <param name="pi_min" type="integer" value="23" label="lower bound of piRNA range"/>
|
|
|
232 <param name="pi_max" type="integer" value="29" label="higher bound of piRNA range"/>
|
|
|
233
|
|
|
234 <param name="mis" type="integer" value="0" label="maximal genome mismatches"/>
|
|
|
235 <param name="misTE" type="integer" value="3" label="maximal TE mismatches"/>
|
|
|
236 <param name="PPPon" type="boolean" checked="true" label="PPPartners"/>
|
|
|
237 </inputs>
|
|
|
238 <outputs>
|
|
|
239 <data format="html" name="html_out" label="${tool.name}_${first_input.name}_${on_string}"/>
|
|
|
240
|
|
|
241 <collection format ="fastqsanger" type="list" label="${tool.name}_fastq_outputs" name="output_fastqsanger">
|
|
|
242 <discover_datasets format ="fastqsanger" pattern="(?P<name>.*)" directory="fastq_dir" />
|
|
|
243 </collection>
|
|
|
244
|
|
|
245 </outputs>
|
|
|
246 <help>
|
|
|
247 **User manual**
|
|
|
248 "https://github.com/brassetjensen/sRNAPipe/blob/master/sRNAPipe_User_Manual.pdf"
|
|
|
249 </help>
|
|
|
250 </tool>
|
