Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowse_hub.xml @ 4:7e471cdd9e71 draft

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planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 8d93b27353190eb23490c9480e560d84cb60c973
author yating-l
date Fri, 07 Jul 2017 16:17:57 -0400
parents 25ad6770359e
children e762f4b9e4bd
comparison
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3:eda851e52060 4:7e471cdd9e71
1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0"> 1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="1.0.0">
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>
78 #end if 78 #end if
79 #if $f.formatChoice.format_select == 'blastxml' 79 #if $f.formatChoice.format_select == 'blastxml'
80 --blastxml $f.formatChoice.BlastXML 80 --blastxml $f.formatChoice.BlastXML
81 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict) 81 #silent $prepare_json($f.formatChoice.BlastXML, extra_data_dict)
82 #end if 82 #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
83 #if $f.formatChoice.format_select == 'gtf' 87 #if $f.formatChoice.format_select == 'gtf'
84 --gtf $f.formatChoice.GTF 88 --gtf $f.formatChoice.GTF
85 #set track_color = str($f.formatChoice.track_color) 89 #set track_color = str($f.formatChoice.track_color)
86 #silent extra_data_dict.update({"color" : $track_color}) 90 #silent extra_data_dict.update({"color" : $track_color})
87 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict) 91 #silent $prepare_json($f.formatChoice.GTF, extra_data_dict)
112 <repeat name="format" title="New track"> 116 <repeat name="format" title="New track">
113 <conditional name="formatChoice"> 117 <conditional name="formatChoice">
114 <param name="format_select" type="select" label="Format"> 118 <param name="format_select" type="select" label="Format">
115 <option value="bam" selected="true">BAM</option> 119 <option value="bam" selected="true">BAM</option>
116 <option value="bed">BED</option> 120 <option value="bed">BED</option>
117 <option value="blastxml">BLASTXML</option> 121 <option value="blastxml">BlastXML</option>
118 <option value="bigwig">BIGWIG</option> 122 <option value="bigpsl">BigPsl</option>
123 <option value="bigwig">BigWig</option>
119 <option value="gff3">GFF3</option> 124 <option value="gff3">GFF3</option>
120 <option value="gtf">GTF</option> 125 <option value="gtf">GTF</option>
121 </param> 126 </param>
122 127
123 <when value="bam"> 128 <when value="bam">
177 type="data" 182 type="data"
178 label="Blast Alignments File" 183 label="Blast Alignments File"
179 /> 184 />
180 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" /> 185 <param name="label" type="text" size="30" value="Blast Alignment" label="Track name" />
181 </when> 186 </when>
187 <when value="bigpsl">
188 <param
189 format="bigpsl"
190 name="BigPsl"
191 type="data"
192 label="Blat Alignments File"
193 />
194 <param name="label" type="text" size="30" value="Blat Alignment" label="Track name" />
195 </when>
182 <when value="bigwig"> 196 <when value="bigwig">
183 <param 197 <param
184 format="bigwig" 198 format="bigwig"
185 name="BIGWIG" 199 name="BIGWIG"
186 type="data" 200 type="data"
263 </repeat> 277 </repeat>
264 </repeat> 278 </repeat>
265 </inputs> 279 </inputs>
266 280
267 <outputs> 281 <outputs>
268 <data format="html" name="output" label="${tool.name}" /> 282 <data format="jbrowsehub" name="output" label="${tool.name}" />
269 </outputs> 283 </outputs>
270 <tests> 284 <tests>
271 <test> 285 <test>
272 <param name="reference" value="dbia3/raw/dbia3.fa" /> 286 <param name="reference" value="dbia3/raw/dbia3.fa" />
273 <param name="genome_name" value="unknown" /> 287 <param name="genome_name" value="unknown" />