Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowse_hub.xml @ 5:e762f4b9e4bd draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit a3a8cdf5c9b100db56b2534e8718b5fc976435ff
author yating-l
date Fri, 07 Jul 2017 17:21:23 -0400
parents 7e471cdd9e71
children
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4:7e471cdd9e71 5:e762f4b9e4bd
1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0.0"> 1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0.1">
2 <description> 2 <description>
3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse 3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse
4 </description> 4 </description>
5 5
6 <requirements> 6 <requirements>
54 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats 54 --bedSimpleRepeats $f.formatChoice.bedChoice.BED_simple_repeats
55 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict) 55 #silent $prepare_json($f.formatChoice.bedChoice.BED_simple_repeats, extra_data_dict)
56 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option' 56 #elif $f.formatChoice.bedChoice.bed_select == 'bed_splice_junctions_option'
57 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions 57 --bedSpliceJunctions $f.formatChoice.bedChoice.BED_splice_junctions
58 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict) 58 #silent $prepare_json($f.formatChoice.bedChoice.BED_splice_junctions, extra_data_dict)
59 #elif $f.formatChoice.bedChoice.bed_select == 'bigpsl'
60 --bigpsl $f.formatChoice.bedChoice.BigPsl
61 #silent $prepare_json($f.formatChoice.bedChoice.BigPsl, extra_data_dict)
59 #end if 62 #end if
60 #end if 63 #end if
61 #if $f.formatChoice.format_select == 'bam' 64 #if $f.formatChoice.format_select == 'bam'
62 --bam $f.formatChoice.BAM 65 --bam $f.formatChoice.BAM
63 #silent $prepare_json($f.formatChoice.BAM, extra_data_dict) 66 #silent $prepare_json($f.formatChoice.BAM, extra_data_dict)
78 #end if 81 #end if
79 #if $f.formatChoice.format_select == 'blastxml' 82 #if $f.formatChoice.format_select == 'blastxml'
80 --blastxml $f.formatChoice.BlastXML 83 --blastxml $f.formatChoice.BlastXML
81 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict) 84 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
82 #end if 85 #end if
83 #if $f.formatChoice.format_select == 'bigpsl'
84 --bigpsl $f.formatChoice.BigPsl
85 #silent $prepare_json($f.formatChoice.BigPsl, extra_data_dict)
86 #end if
87 #if $f.formatChoice.format_select == 'gtf' 86 #if $f.formatChoice.format_select == 'gtf'
88 --gtf $f.formatChoice.GTF 87 --gtf $f.formatChoice.GTF
89 #set track_color = str($f.formatChoice.track_color) 88 #set track_color = str($f.formatChoice.track_color)
90 #silent extra_data_dict.update({"color" : $track_color}) 89 #silent extra_data_dict.update({"color" : $track_color})
91 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict) 90 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict)
117 <conditional name="formatChoice"> 116 <conditional name="formatChoice">
118 <param name="format_select" type="select" label="Format"> 117 <param name="format_select" type="select" label="Format">
119 <option value="bam" selected="true">BAM</option> 118 <option value="bam" selected="true">BAM</option>
120 <option value="bed">BED</option> 119 <option value="bed">BED</option>
121 <option value="blastxml">BlastXML</option> 120 <option value="blastxml">BlastXML</option>
122 <option value="bigpsl">BigPsl</option>
123 <option value="bigwig">BigWig</option> 121 <option value="bigwig">BigWig</option>
124 <option value="gff3">GFF3</option> 122 <option value="gff3">GFF3</option>
125 <option value="gtf">GTF</option> 123 <option value="gtf">GTF</option>
126 </param> 124 </param>
127 125
138 <conditional name="bedChoice"> 136 <conditional name="bedChoice">
139 <param name="bed_select" type="select" label="Bed Choice"> 137 <param name="bed_select" type="select" label="Bed Choice">
140 <option value="bed_generic_option">BED format</option> 138 <option value="bed_generic_option">BED format</option>
141 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option> 139 <option value="bed_simple_repeats_option">BED Simple repeat (bed4+12 / simpleRepeat.as)</option>
142 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option> 140 <option value="bed_splice_junctions_option">BED Splice junctions (bed12+1 / spliceJunctions.as)</option>
141 <option value="bigpsl">Blat Alignment (bed12+12 / bigPsl.as)</option>
143 </param> 142 </param>
144 <when value="bed_generic_option"> 143 <when value="bed_generic_option">
145 <param 144 <param
146 format="bed" 145 format="bed"
147 name="BED_generic" 146 name="BED_generic"
161 <param 160 <param
162 format="bed" 161 format="bed"
163 name="BED_splice_junctions" 162 name="BED_splice_junctions"
164 type="data" 163 type="data"
165 label="Bed Splice Junctions (Bed12+1) File" 164 label="Bed Splice Junctions (Bed12+1) File"
165 />
166 </when>
167 <when value="bigpsl">
168 <param
169 format="bed"
170 name="BigPsl"
171 type="data"
172 label="Blat Alignments File"
166 /> 173 />
167 </when> 174 </when>
168 </conditional> 175 </conditional>
169 <param name="label" type="text" size="30" value="BED file" label="Track name" /> 176 <param name="label" type="text" size="30" value="BED file" label="Track name" />
170 <param name="track_color" type="color" label="Track color" value="#daa520"> 177 <param name="track_color" type="color" label="Track color" value="#daa520">
181 name="BlastXML" 188 name="BlastXML"
182 type="data" 189 type="data"
183 label="Blast Alignments File" 190 label="Blast Alignments File"
184 /> 191 />
185 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" /> 192 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
186 </when> 193 <param name="track_color" type="color" label="Track color" value="#daa520">
187 <when value="bigpsl"> 194 <sanitizer>
188 <param 195 <valid initial="string.letters,string.digits">
189 format="bigpsl" 196 <add value="#"/>
190 name="BigPsl" 197 </valid>
191 type="data" 198 </sanitizer>
192 label="Blat Alignments File" 199 </param>
193 />
194 <param name="label" type="text" size="30" value="Blat Alignment" label="Track name" />
195 </when> 200 </when>
196 <when value="bigwig"> 201 <when value="bigwig">
197 <param 202 <param
198 format="bigwig" 203 format="bigwig"
199 name="BIGWIG" 204 name="BIGWIG"