Mercurial > repos > rmarenco > hubarchivecreator

comparison hubArchiveCreator.xml @ 16:3233451a3bd6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit fc73ec22a0db3ab09c4ac13dc58f0b54ae37845c
author rmarenco
date Sun, 25 Sep 2016 11:25:38 -0400
parents 2a45cd656e8e
children c02720d1afee
comparison
equal deleted inserted replaced
15:2a45cd656e8e 16:3233451a3bd6
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 <requirement type="package" version="332">ucsc-twobitinfo</requirement> 16 <requirement type="package" version="332">ucsc-twobitinfo</requirement>
16 <requirement type="package" version="1.3">samtools</requirement> 17 <requirement type="package" version="1.3">samtools</requirement>
17 <!-- ToolShed dependencies --> 18 <!-- ToolShed dependencies -->
18 <requirement type="package" version="312">ucsc_tools</requirement> 19 <requirement type="package" version="312">ucsc_tools</requirement>
19 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement> 20 <requirement type="package" version="0.0.1">gff3ToGenePred</requirement>
58 #silent $data_parameter_dict.update({$false_path: $data_dict}) 59 #silent $data_parameter_dict.update({$false_path: $data_dict})
59 60
60 #end def 61 #end def
61 62
62 #for $i, $f in enumerate( $format ) 63 #for $i, $f in enumerate( $format )
64 #set track_color = str($f.formatChoice.track_color)
65
63 #if $f.formatChoice.format_select == "bam" 66 #if $f.formatChoice.format_select == "bam"
64 --bam $f.formatChoice.BAM 67 --bam $f.formatChoice.BAM
65 #set bam_index = $f.formatChoice.BAM.metadata.bam_index 68 #set bam_index = $f.formatChoice.BAM.metadata.bam_index
66 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index}) 69 #silent $prepare_json($f.formatChoice.BAM, $i, {"index": $bam_index,
70 "track_color": $track_color})
67 #end if 71 #end if
68 #if $f.formatChoice.format_select == "bed" 72 #if $f.formatChoice.format_select == "bed"
69 #if $f.formatChoice.bedChoice.bed_select == "bed" 73 #if $f.formatChoice.bedChoice.bed_select == "bed"
70 --bed $f.formatChoice.bedChoice.BED 74 --bed $f.formatChoice.bedChoice.BED
71 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i) 75 #silent $prepare_json($f.formatChoice.bedChoice.BED, $i,
76 {"track_color": $track_color})
72 #end if 77 #end if
73 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option" 78 #if $f.formatChoice.bedChoice.bed_select == "bed_simple_repeats_option"
74 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats 79 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
75 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i) 80 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, $i,
81 {"track_color": $track_color})
76 #end if 82 #end if
83 #end if
84 #if $f.formatChoice.format_select == "psl"
85 --psl $f.formatChoice.PSL
86 #silent $prepare_json($f.formatChoice.PSL, $i,
87 {"track_color": $track_color})
77 #end if 88 #end if
78 #if $f.formatChoice.format_select == "bigwig" 89 #if $f.formatChoice.format_select == "bigwig"
79 --bigwig $f.formatChoice.BIGWIG 90 --bigwig $f.formatChoice.BIGWIG
80 #silent $prepare_json($f.formatChoice.BIGWIG, $i) 91 #silent $prepare_json($f.formatChoice.BIGWIG, $i,
92 {"track_color": $track_color})
81 #end if 93 #end if
82 #if $f.formatChoice.format_select == "gff3" 94 #if $f.formatChoice.format_select == "gff3"
83 --gff3 $f.formatChoice.GFF3 95 --gff3 $f.formatChoice.GFF3
84 #silent $prepare_json($f.formatChoice.GFF3, $i) 96 #silent $prepare_json($f.formatChoice.GFF3, $i,
97 {"track_color": $track_color})
85 #end if 98 #end if
86 #if $f.formatChoice.format_select == "gtf" 99 #if $f.formatChoice.format_select == "gtf"
87 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8 100 ## Add also GTF from Agustus? See https://github.com/ENCODE-DCC/kentUtils/issues/8
88 --gtf $f.formatChoice.GTF 101 --gtf $f.formatChoice.GTF
89 #silent $prepare_json($f.formatChoice.GTF, $i) 102 #silent $prepare_json($f.formatChoice.GTF, $i,
103 {"track_color": $track_color})
90 #end if 104 #end if
91 #end for 105 #end for
92 106
93 ## We combine the fasta file dataset name with his false path in a JSON object 107 ## We combine the fasta file dataset name with his false path in a JSON object
94 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name}) 108 #set fasta_json = json.dumps({"false_path": str($fasta_file), "name": $fasta_file.name})
128 <repeat name="format" title="Formats"> 142 <repeat name="format" title="Formats">
129 <conditional name="formatChoice"> 143 <conditional name="formatChoice">
130 <param name="format_select" type="select" label="Format"> 144 <param name="format_select" type="select" label="Format">
131 <option value="bam" selected="true">BAM</option> 145 <option value="bam" selected="true">BAM</option>
132 <option value="bed">BED</option> 146 <option value="bed">BED</option>
147 <option value="psl">PSL</option>
133 <option value="bigwig">BIGWIG</option> 148 <option value="bigwig">BIGWIG</option>
134 <option value="gff3">GFF3</option> 149 <option value="gff3">GFF3</option>
135 <option value="gtf">GTF</option> 150 <option value="gtf">GTF</option>
136 </param> 151 </param>
137 152
140 format="bam" 155 format="bam"
141 name="BAM" 156 name="BAM"
142 type="data" 157 type="data"
143 label="BAM File" 158 label="BAM File"
144 /> 159 />
145 </when> 160 <!-- TODO: Find a solution to avoid repetition and to generate a new color depending on the others -->
146 <when value="bigwig"> 161 <param name="track_color" type="color" label="Track color" value="#000000">
147 <param 162 <sanitizer>
148 format="bigwig" 163 <valid initial="string.letters,string.digits">
149 name="BIGWIG" 164 <add value="#"/>
150 type="data" 165 </valid>
151 label="BIGWIG File" 166 </sanitizer>
152 /> 167 </param>
153 </when>
154 <when value="gff3">
155 <param
156 format="gff3"
157 name="GFF3"
158 type="data"
159 label="GFF3 File"
160 />
161 </when>
162 <when value="gtf">
163 <param
164 format="gtf"
165 name="GTF"
166 type="data"
167 label="GTF File"
168 />
169 </when> 168 </when>
170 <when value="bed"> 169 <when value="bed">
171 <conditional name="bedChoice"> 170 <conditional name="bedChoice">
172 <param name="bed_select" type="select" label="Bed Choice"> 171 <param name="bed_select" type="select" label="Bed Choice">
173 <option value="bed" selected="true">BED Generic (bed3+)</option> 172 <option value="bed" selected="true">BED Generic (bed3+)</option>
178 format="bed" 177 format="bed"
179 name="BED" 178 name="BED"
180 type="data" 179 type="data"
181 label="Generic Bed File Choice" 180 label="Generic Bed File Choice"
182 /> 181 />
182
183 </when> 183 </when>
184 <when value="bed_simple_repeats_option"> 184 <when value="bed_simple_repeats_option">
185 <param 185 <param
186 format="bed" 186 format="bed"
187 name="BED_simple_repeats" 187 name="BED_simple_repeats"
188 type="data" 188 type="data"
189 label="Bed Simple Repeats (Bed4+12) File" 189 label="Bed Simple Repeats (Bed4+12) File"
190 /> 190 />
191 </when> 191 </when>
192 </conditional> 192 </conditional>
193 <param name="track_color" type="color" label="Track color" value="#000000">
194 <sanitizer>
195 <valid initial="string.letters,string.digits">
196 <add value="#"/>
197 </valid>
198 </sanitizer>
199 </param>
200 </when>
201 <when value="psl">
202 <param
203 format="psl"
204 name="PSL"
205 type="data"
206 label="PSL File"
207 />
208 <param name="track_color" type="color" label="Track color" value="#000000">
209 <sanitizer>
210 <valid initial="string.letters,string.digits">
211 <add value="#"/>
212 </valid>
213 </sanitizer>
214 </param>
215 </when>
216 <when value="bigwig">
217 <param
218 format="bigwig"
219 name="BIGWIG"
220 type="data"
221 label="BIGWIG File"
222 />
223 <param name="track_color" type="color" label="Track color" value="#000000">
224 <sanitizer>
225 <valid initial="string.letters,string.digits">
226 <add value="#"/>
227 </valid>
228 </sanitizer>
229 </param>
230 </when>
231 <when value="gff3">
232 <param
233 format="gff3"
234 name="GFF3"
235 type="data"
236 label="GFF3 File"
237 />
238 <param name="track_color" type="color" label="Track color" value="#000000">
239 <sanitizer>
240 <valid initial="string.letters,string.digits">
241 <add value="#"/>
242 </valid>
243 </sanitizer>
244 </param>
245 </when>
246 <when value="gtf">
247 <param
248 format="gtf"
249 name="GTF"
250 type="data"
251 label="GTF File"
252 />
253 <param name="track_color" type="color" label="Track color" value="#000000">
254 <sanitizer>
255 <valid initial="string.letters,string.digits">
256 <add value="#"/>
257 </valid>
258 </sanitizer>
259 </param>
193 </when> 260 </when>
194 </conditional> 261 </conditional>
195 </repeat> 262 </repeat>
196 <conditional name="advanced_options"> 263 <conditional name="advanced_options">
197 <param name="advanced_options_selector" type="select" label="Advanced options"> 264 <param name="advanced_options_selector" type="select" label="Advanced options">