Mercurial > repos > yating-l > jbrowsearchivecreator

comparison jbrowseArchiveCreator.xml @ 14:3f9971a91096 draft

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planemo upload for repository https://github.com/goeckslab/jbrowse-archive-creator.git commit e526b4e8bef4677b832e940bacb8969a18efc3e3
author yating-l
date Wed, 20 Jun 2018 17:24:45 -0400
parents 43a700afd457
children 6464399df918
comparison
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13:43a700afd457 14:3f9971a91096
1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.2.1"> 1 <tool id="jbrowse_hub" name="JBrowse Archive Creator" version="2.3.0">
2 <description> 2 <description>
3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin 3 This Galaxy tool is used to prepare your files to be ready for displaying on JBrowse with Apollo plugin
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
106 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option" 106 #if $f.formatChoice.bedChoice.bed_select == "bed_splice_junctions_option"
107 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final, 107 #silent $prepare_json("BedSpliceJunctions", $f.formatChoice.bedChoice.BED_splice_junctions, $index_track_final,
108 $extra_data_dict) 108 $extra_data_dict)
109 #end if 109 #end if
110 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option" 110 #if $f.formatChoice.bedChoice.bed_select == "bed_blast_alignment_option"
111 ##set database = str($f.formatChoice.bedChoice.database) 111 #set database = str($f.formatChoice.bedChoice.database)
112 ##silent $extra_data_dict.update({"database": $database}) 112 #silent $extra_data_dict.update({"database": $database})
113 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final, 113 #silent $prepare_json("BedBlastAlignments", $f.formatChoice.bedChoice.BED_blast_alignment, $index_track_final,
114 $extra_data_dict) 114 $extra_data_dict)
115 #end if 115 #end if
116 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option" 116 #if $f.formatChoice.bedChoice.bed_select == "bed_blat_alignment_option"
117 ##set database = str($f.formatChoice.bedChoice.database) 117 #set database = str($f.formatChoice.bedChoice.database)
118 ##silent $extra_data_dict.update({"database": $database}) 118 #silent $extra_data_dict.update({"database": $database})
119 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final, 119 #silent $prepare_json("BedBlatAlignments", $f.formatChoice.bedChoice.BED_blat_alignment, $index_track_final,
120 $extra_data_dict) 120 $extra_data_dict)
121 #end if 121 #end if
122 #end if 122 #end if
123 #if $f.formatChoice.format_select == "blastxml" 123 #if $f.formatChoice.format_select == "blastxml"
124 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)}) 124 #set database = str($f.formatChoice.database)
125 #silent $extra_data_dict.update({"database": $database, "nameIndex": str($f.formatChoice.nameIndex)})
125 #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final, 126 #silent $prepare_json("BlastXml", $f.formatChoice.BlastXML, $index_track_final,
126 extra_data_dict) 127 extra_data_dict)
127 #end if 128 #end if
128 #if $f.formatChoice.format_select == "bigwig" 129 #if $f.formatChoice.format_select == "bigwig"
129 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)}) 130 #silent $extra_data_dict.update({"nameIndex": str($f.formatChoice.nameIndex)})
249 format="bed" 250 format="bed"
250 name="BED_blast_alignment" 251 name="BED_blast_alignment"
251 type="data" 252 type="data"
252 label="Bed Blast Alignments (Bed12+12) File" 253 label="Bed Blast Alignments (Bed12+12) File"
253 /> 254 />
255 <param name="database" type="select" label="Protein database">
256 <option value="NCBI" selected="true">NCBI</option>
257 <option value="UniProt">UniProt</option>
258 <option value="FlyBase">FlyBase</option>
259 <option value="Others">Others</option>
260 </param>
254 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> 261 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
255 </when> 262 </when>
256 <when value="bed_blat_alignment_option"> 263 <when value="bed_blat_alignment_option">
257 <param 264 <param
258 format="bed" 265 format="bed"
259 name="BED_blat_alignment" 266 name="BED_blat_alignment"
260 type="data" 267 type="data"
261 label="Bed BLAT Alignments (bigPsl) File" 268 label="Bed BLAT Alignments (bigPsl) File"
262 /> 269 />
270 <param name="database" type="select" label="mRNA database">
271 <option value="NCBI" selected="true">NCBI</option>
272 <option value="Others">Others</option>
273 </param>
263 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" /> 274 <param name="nameIndex" type="boolean" checked="true" label="Do you want to builds name indexes for this track to enable search for a feature by name" />
264 </when> 275 </when>
265 </conditional> 276 </conditional>
266 <param name="longLabel" type="text" size="30" label="Track label" /> 277 <param name="longLabel" type="text" size="30" label="Track label" />
267 <param name="track_color" type="color" label="Track color" value="#000000"> 278 <param name="track_color" type="color" label="Track color" value="#000000">
277 format="blastxml" 288 format="blastxml"
278 name="BlastXML" 289 name="BlastXML"
279 type="data" 290 type="data"
280 label="Blast Alignments File" 291 label="Blast Alignments File"
281 /> 292 />
293 <param name="database" type="select" label="Protein database">
294 <option value="NCBI" selected="true">NCBI</option>
295 <option value="UniProt">UniProt</option>
296 <option value="FlyBase">FlyBase</option>
297 <option value="Others">Others</option>
298 </param>
282 <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" /> 299 <param name="longLabel" type="text" size="30" value="Blast Alignment" label="Track label" />
283 <param name="track_color" type="color" label="Track color" value="#000000"> 300 <param name="track_color" type="color" label="Track color" value="#000000">
284 <sanitizer> 301 <sanitizer>
285 <valid initial="string.letters,string.digits"> 302 <valid initial="string.letters,string.digits">
286 <add value="#"/> 303 <add value="#"/>