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comparison hubArchiveCreator.xml @ 17:c02720d1afee draft

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planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit 1adbf397de1fc7af4d91e026093d7fff983e21cf
author rmarenco
date Fri, 30 Sep 2016 15:14:24 -0400
parents 3233451a3bd6
children d786bca6a75d
comparison
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16:3233451a3bd6 17:c02720d1afee
10 <requirement type="package" version="332">ucsc-fatotwobit</requirement> 10 <requirement type="package" version="332">ucsc-fatotwobit</requirement>
11 <requirement type="package" version="332">ucsc-genepredtobed</requirement> 11 <requirement type="package" version="332">ucsc-genepredtobed</requirement>
12 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement> 12 <requirement type="package" version="332">ucsc-genepredtobiggenepred</requirement>
13 <requirement type="package" version="332">ucsc-gff3togenepred</requirement> 13 <requirement type="package" version="332">ucsc-gff3togenepred</requirement>
14 <requirement type="package" version="332">ucsc-gtftogenepred</requirement> 14 <requirement type="package" version="332">ucsc-gtftogenepred</requirement>
15 <requirement type="package" version="332">ucsc-psltobigpsl</requirement> 15 <!-- TODO: Change the conda ucsc-psltobigpsl and take one > v337 because of bugs before -->
16 <!-- <requirement type="package" version="332">ucsc-psltobigpsl</requirement> -->
16 <requirement type="package" version="332">ucsc-twobitinfo</requirement> 17 <requirement type="package" version="332">ucsc-twobitinfo</requirement>
17 <requirement type="package" version="1.3">samtools</requirement> 18 <requirement type="package" version="1.3">samtools</requirement>
18 <!-- ToolShed dependencies --> 19 <!-- ToolShed dependencies -->
19 <requirement type="package" version="312">ucsc_tools</requirement> 20 <requirement type="package" version="312">ucsc_tools</requirement>
20 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement> 21 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
21 <requirement type="package" version="0.0.1">gtfToGenePred</requirement> 22 <requirement type="package" version="0.0.1">gtfToGenePred</requirement>
22 <requirement type="package" version="0.0.1">genePredToBed</requirement> 23 <requirement type="package" version="0.0.1">genePredToBed</requirement>
23 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement> 24 <requirement type="package" version="0.0.1">genePredToBigGenePred</requirement>
25 <requirement type="package" version="0.0.1">pslToBigPsl</requirement>
24 <requirement type="package" version="1.2">samtools</requirement> 26 <requirement type="package" version="1.2">samtools</requirement>
25 </requirements> 27 </requirements>
26 28
27 <stdio> 29 <stdio>
28 <regex match="^pass1" 30 <regex match="^pass1"
58 60
59 #silent $data_parameter_dict.update({$false_path: $data_dict}) 61 #silent $data_parameter_dict.update({$false_path: $data_dict})
60 62
61 #end def 63 #end def
62 64
63 #for $i, $f in enumerate( $format ) 65 #for $i_g, $g in enumerate( $group )
64 #set track_color = str($f.formatChoice.track_color) 66 #for $i, $f in enumerate( $g.format )
65 67
66 #if $f.formatChoice.format_select == "bam" 68 ## For each format, we have a few mandatory fields we store in a dict
67 --bam $f.formatChoice.BAM 69 #set track_color = str($f.formatChoice.track_color)
68 #set bam_index = $f.formatChoice.BAM.metadata.bam_index 70 #set group_name = str($g.group_name)
69 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index, 71
70 "track_color": $track_color}) 72 #set extra_data_dict = {"track_color": $track_color,
71 #end if 73 "group_name": $group_name}
72 #if $f.formatChoice.format_select == "bed" 74
73 #if $f.formatChoice.bedChoice.bed_select == "bed" 75 #if $f.formatChoice.format_select == "bam"
74 --bed $f.formatChoice.bedChoice.BED 76 --bam $f.formatChoice.BAM
75 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i, 77 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
76 {"track_color": $track_color}) 78
77 #end if 79 ## Add Bam format specific fields
78 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" 80 #silent extra_data_dict.update({"index": $bam_index})
79 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats 81
80 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i, 82 #silent $prepare_json($f.formatChoice.BAM, $i, extra_data_dict)
81 {"track_color": $track_color}) 83 #end if
82 #end if 84 #if $f.formatChoice.format_select == "bed"
83 #end if 85 #if $f.formatChoice.bedChoice.bed_select == "bed"
84 #if $f.formatChoice.format_select == "psl" 86 --bed $f.formatChoice.bedChoice.BED
85 --psl $f.formatChoice.PSL 87 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i,
86 #silent $prepare_json($f.formatChoice.PSL, $i, 88 extra_data_dict)
87 {"track_color": $track_color}) 89 #end if
88 #end if 90 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
89 #if $f.formatChoice.format_select == "bigwig" 91 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
90 --bigwig $f.formatChoice.BIGWIG 92 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i,
91 #silent $prepare_json($f.formatChoice.BIGWIG, $i, 93 extra_data_dict)
92 {"track_color": $track_color}) 94 #end if
93 #end if 95 #end if
94 #if $f.formatChoice.format_select == "gff3" 96 #if $f.formatChoice.format_select == "psl"
95 --gff3 $f.formatChoice.GFF3 97 --psl $f.formatChoice.PSL
96 #silent $prepare_json($f.formatChoice.GFF3, $i, 98 #silent $prepare_json($f.formatChoice.PSL, $i,
97 {"track_color": $track_color}) 99 extra_data_dict)
98 #end if 100 #end if
99 #if $f.formatChoice.format_select == "gtf" 101 #if $f.formatChoice.format_select == "bigwig"
100 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 102 --bigwig $f.formatChoice.BIGWIG
101 --gtf $f.formatChoice.GTF 103 #silent $prepare_json($f.formatChoice.BIGWIG, $i,
102 #silent $prepare_json($f.formatChoice.GTF, $i, 104 extra_data_dict)
103 {"track_color": $track_color}) 105 #end if
104 #end if 106 #if $f.formatChoice.format_select == "gff3"
107 --gff3 $f.formatChoice.GFF3
108 #silent $prepare_json($f.formatChoice.GFF3, $i,
109 extra_data_dict)
110 #end if
111 #if $f.formatChoice.format_select == "gtf"
112 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
113 --gtf $f.formatChoice.GTF
114 #silent $prepare_json($f.formatChoice.GTF, $i,
115 extra_data_dict)
116 #end if
117 #end for
105 #end for 118 #end for
106 119
107 ## We combine the fasta file dataset name with his false path in a JSON object 120 ## We combine the fasta file dataset name with his false path in a JSON object
108 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name}) 121 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
109 -f '$fasta_json' 122 -f '$fasta_json'
137 format="fasta" 150 format="fasta"
138 name="fasta_file" 151 name="fasta_file"
139 type="data" 152 type="data"
140 label="Reference genome" 153 label="Reference genome"
141 /> 154 />
142 <repeat name="format" title="Formats"> 155 <repeat name="group" title="New group">
143 <conditional name="formatChoice"> 156 <param type="text" name="group_name" label="Group name" value="Default group"/>
144 <param name="format_select" type="select" label="Format"> 157 <repeat name="format" title="New track">
145 <option value="bam" selected="true">BAM</option> 158 <conditional name="formatChoice">
146 <option value="bed">BED</option> 159 <param name="format_select" type="select" label="Format">
147 <option value="psl">PSL</option> 160 <option value="bam" selected="true">BAM</option>
148 <option value="bigwig">BIGWIG</option> 161 <option value="bed">BED</option>
149 <option value="gff3">GFF3</option> 162 <option value="psl">PSL</option>
150 <option value="gtf">GTF</option> 163 <option value="bigwig">BIGWIG</option>
151 </param> 164 <option value="gff3">GFF3</option>
152 165 <option value="gtf">GTF</option>
153 <when value="bam">
154 <param
155 format="bam"
156 name="BAM"
157 type="data"
158 label="BAM File"
159 />
160 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
161 <param name="track_color" type="color" label="Track color" value="#000000">
162 <sanitizer>
163 <valid initial="string.letters,string.digits">
164 <add value="#"/>
165 </valid>
166 </sanitizer>
167 </param> 166 </param>
168 </when> 167
169 <when value="bed"> 168 <when value="bam">
170 <conditional name="bedChoice"> 169 <param
171 <param name="bed_select" type="select" label="Bed Choice"> 170 format="bam"
172 <option value="bed" selected="true">BED Generic (bed3+)</option> 171 name="BAM"
173 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> 172 type="data"
174 </param> 173 label="BAM File"
175 <when value="bed"> 174 />
176 <param 175 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
177 format="bed" 176 <param name="track_color" type="color" label="Track color" value="#000000">
178 name="BED" 177 <sanitizer>
179 type="data" 178 <valid initial="string.letters,string.digits">
180 label="Generic Bed File Choice" 179 <add value="#"/>
181 /> 180 </valid>
182 181 </sanitizer>
183 </when> 182 </param>
184 <when value="bed_simple_repeats_option"> 183 </when>
185 <param 184 <when value="bed">
186 format="bed" 185 <conditional name="bedChoice">
187 name="BED_simple_repeats" 186 <param name="bed_select" type="select" label="Bed Choice">
188 type="data" 187 <option value="bed" selected="true">BED Generic (bed3+)</option>
189 label="Bed Simple Repeats (Bed4+12) File" 188 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
190 /> 189 </param>
191 </when> 190 <when value="bed">
192 </conditional> 191 <param
193 <param name="track_color" type="color" label="Track color" value="#000000"> 192 format="bed"
194 <sanitizer> 193 name="BED"
195 <valid initial="string.letters,string.digits"> 194 type="data"
196 <add value="#"/> 195 label="Generic Bed File Choice"
197 </valid> 196 />
198 </sanitizer> 197
199 </param> 198 </when>
200 </when> 199 <when value="bed_simple_repeats_option">
201 <when value="psl"> 200 <param
202 <param 201 format="bed"
203 format="psl" 202 name="BED_simple_repeats"
204 name="PSL" 203 type="data"
205 type="data" 204 label="Bed Simple Repeats (Bed4+12) File"
206 label="PSL File" 205 />
207 /> 206 </when>
208 <param name="track_color" type="color" label="Track color" value="#000000"> 207 </conditional>
209 <sanitizer> 208 <param name="track_color" type="color" label="Track color" value="#000000">
210 <valid initial="string.letters,string.digits"> 209 <sanitizer>
211 <add value="#"/> 210 <valid initial="string.letters,string.digits">
212 </valid> 211 <add value="#"/>
213 </sanitizer> 212 </valid>
214 </param> 213 </sanitizer>
215 </when> 214 </param>
216 <when value="bigwig"> 215 </when>
217 <param 216 <when value="psl">
218 format="bigwig" 217 <param
219 name="BIGWIG" 218 format="psl"
220 type="data" 219 name="PSL"
221 label="BIGWIG File" 220 type="data"
222 /> 221 label="PSL File"
223 <param name="track_color" type="color" label="Track color" value="#000000"> 222 />
224 <sanitizer> 223 <param name="track_color" type="color" label="Track color" value="#000000">
225 <valid initial="string.letters,string.digits"> 224 <sanitizer>
226 <add value="#"/> 225 <valid initial="string.letters,string.digits">
227 </valid> 226 <add value="#"/>
228 </sanitizer> 227 </valid>
229 </param> 228 </sanitizer>
230 </when> 229 </param>
231 <when value="gff3"> 230 </when>
232 <param 231 <when value="bigwig">
233 format="gff3" 232 <param
234 name="GFF3" 233 format="bigwig"
235 type="data" 234 name="BIGWIG"
236 label="GFF3 File" 235 type="data"
237 /> 236 label="BIGWIG File"
238 <param name="track_color" type="color" label="Track color" value="#000000"> 237 />
239 <sanitizer> 238 <param name="track_color" type="color" label="Track color" value="#000000">
240 <valid initial="string.letters,string.digits"> 239 <sanitizer>
241 <add value="#"/> 240 <valid initial="string.letters,string.digits">
242 </valid> 241 <add value="#"/>
243 </sanitizer> 242 </valid>
244 </param> 243 </sanitizer>
245 </when> 244 </param>
246 <when value="gtf"> 245 </when>
247 <param 246 <when value="gff3">
248 format="gtf" 247 <param
249 name="GTF" 248 format="gff3"
250 type="data" 249 name="GFF3"
251 label="GTF File" 250 type="data"
252 /> 251 label="GFF3 File"
253 <param name="track_color" type="color" label="Track color" value="#000000"> 252 />
254 <sanitizer> 253 <param name="track_color" type="color" label="Track color" value="#000000">
255 <valid initial="string.letters,string.digits"> 254 <sanitizer>
256 <add value="#"/> 255 <valid initial="string.letters,string.digits">
257 </valid> 256 <add value="#"/>
258 </sanitizer> 257 </valid>
259 </param> 258 </sanitizer>
260 </when> 259 </param>
261 </conditional> 260 </when>
261 <when value="gtf">
262 <param
263 format="gtf"
264 name="GTF"
265 type="data"
266 label="GTF File"
267 />
268 <param name="track_color" type="color" label="Track color" value="#000000">
269 <sanitizer>
270 <valid initial="string.letters,string.digits">
271 <add value="#"/>
272 </valid>
273 </sanitizer>
274 </param>
275 </when>
276 </conditional>
277 </repeat>
262 </repeat> 278 </repeat>
263 <conditional name="advanced_options"> 279 <conditional name="advanced_options">
264 <param name="advanced_options_selector" type="select" label="Advanced options"> 280 <param name="advanced_options_selector" type="select" label="Advanced options">
265 <option value="off" selected="true">Hide advanced options</option> 281 <option value="off" selected="true">Hide advanced options</option>
266 <option value="on">Display advanced options</option> 282 <option value="on">Display advanced options</option>