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comparison jbrowse.xml @ 6:ecbdfc775b9a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit fe77b125826ab5cbd0a235f957d66e544b658a98
author iuc
date Sat, 25 Jun 2016 16:44:39 -0400
parents ae9382cfb6ac
children ad4b9d7eae6a
comparison
equal deleted inserted replaced
5:ae9382cfb6ac 6:ecbdfc775b9a
1 <tool id="jbrowse" name="JBrowse" version="0.5"> 1 <tool id="jbrowse" name="JBrowse" version="0.5.2">
2 <description>genome browser</description> 2 <description>genome browser</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
70 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> 70 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?>
71 <root> 71 <root>
72 <metadata> 72 <metadata>
73 <gencode>$gencode</gencode> 73 <gencode>$gencode</gencode>
74 <genomes> 74 <genomes>
75 #if str($action.genomes) != "None": 75 #if str($action.reference_genome.genome_type_select) == "indexed":
76 #for $genome in $action.genomes: 76 <genome>${action.reference_genome.genomes.fields.path}</genome>
77 <genome>$genome</genome> 77 #else
78 #end for 78 #for $genome in $action.reference_genome.genomes:
79 #end if 79 <genome>$genome</genome>
80 #end for
81 #end if
80 </genomes> 82 </genomes>
81 <general> 83 <general>
82 <defaultLocation>${jbgen.defaultLocation}</defaultLocation> 84 <defaultLocation>${jbgen.defaultLocation}</defaultLocation>
83 <trackPadding>${jbgen.trackPadding}</trackPadding> 85 <trackPadding>${jbgen.trackPadding}</trackPadding>
84 86
222 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select"> 224 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select">
223 <option value="create">New JBrowse Instance</option> 225 <option value="create">New JBrowse Instance</option>
224 <option value="update">Update exising JBrowse Instance</option> 226 <option value="update">Update exising JBrowse Instance</option>
225 </param> 227 </param>
226 <when value="create"> 228 <when value="create">
227 <param label="Fasta Sequence(s)" 229 <expand macro="genome_selector" />
228 name="genomes"
229 type="data"
230 format="fasta"
231 multiple="True"/>
232 </when> 230 </when>
233 <when value="update"> 231 <when value="update">
234 <param label="Additional Fasta Sequence(s)" 232 <expand macro="genome_selector"
235 help="If sequences are selected, they will be added to the existing JBrowse instance. You should not select any sequences if you are simply updating an existing JBrowse instance which already has the required reference sequences." 233 label="Additional Fasta Sequence(s)"
236 name="genomes" 234 help="If sequences are selected, they will be added to the existing JBrowse instance. You should not select any sequences if you are simply updating an existing JBrowse instance which already has the required reference sequences."
237 type="data" 235 optional="True"/>
238 format="fasta"
239 optional="True"
240 multiple="True"/>
241 <param label="Previous JBrowse Instance" 236 <param label="Previous JBrowse Instance"
242 name="update_jbrowse" 237 name="update_jbrowse"
243 type="data" 238 type="data"
244 format="html" /> 239 format="html" />
245 </when> 240 </when>