Mercurial > repos > bgruening > jbrowse2
annotate jbrowse2.xml @ 0:53c2be00bb6f draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
author | bgruening |
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date | Wed, 05 Jun 2024 08:15:49 +0000 |
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53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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2 <description>genome browser</description> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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3 <macros> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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4 <import>macros.xml</import> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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5 </macros> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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6 <expand macro="edamInc"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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7 <xrefs> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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8 <xref type="bio.tools">jbrowse2</xref> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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9 </xrefs> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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10 <expand macro="requirements"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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11 <required_files> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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12 <include path="autogenJB2.py"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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13 <include path="blastxml_to_gapped_gff3.py"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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14 <include path="convertMAF.sh"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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15 <include path="gff3_rebase.py"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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16 <include path="jb2_webserver.py"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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17 <include path="jbrowse2.py"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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18 <include path="maf2bed.py"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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19 </required_files> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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20 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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21 <command detect_errors="aggressive"><![CDATA[ |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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22 mkdir -p '$output.files_path' && |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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23 cp '$trackxml' '$output.files_path/galaxy.xml' && |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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24 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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25 #if $jbgen.ucol.formcoll=="collect": |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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26 python '$__tool_directory__/autogenJB2.py' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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27 #for $key in $autoCollection.keys(): |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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28 #if $autoCollection[$key].is_collection: |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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29 #set subCol=$autoCollection[$key] |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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30 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf'] |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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31 #if len($pafs) > 0: |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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32 --pafmeta '$pafs[0]' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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33 #set refs = [($pafs[0][2],$subCol[x],x) for x in $subCol.keys() if $subCol[x].ext == 'fasta'] |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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34 #for $ref in $refs: |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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35 --pafreferencemeta '$ref' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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36 #end for |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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37 #end if |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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38 #else if $autoCollection[$key].ext == 'fasta': |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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39 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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40 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf'] |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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41 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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42 #else if $autoCollection[$key].ext in ['bam',] |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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43 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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44 #else if $autoCollection[$key].ext in ['cram',] |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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45 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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46 #end if |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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47 #end for |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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48 --outdir '$output.files_path' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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49 --jbrowse2path \${JBROWSE2_PATH} |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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50 --sessName "Autogen JBrowse" && |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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51 #if $jbgen.zipOut == "true": |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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52 cd '$output.files_path' && |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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53 zip -r - . > '$output' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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54 #else |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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55 cp '$output.files_path/index.html' '$output' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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56 #end if |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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57 #else: |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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58 python '$__tool_directory__/jbrowse2.py' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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59 --jbrowse2path \${JBROWSE2_PATH} |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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60 --outdir '$output.files_path' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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61 --xml '$trackxml' && |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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62 #if $jbgen.zipOut == "true": |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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63 cd '$output.files_path' && |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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64 zip -r - . > '$output' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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65 #else |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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66 cp '$output.files_path/index.html' '$output' |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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67 #end if |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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68 #end if |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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69 ]]></command> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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70 <configfiles> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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71 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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72 <root> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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73 <metadata> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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74 <general> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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75 <defaultLocation>${jbgen.defaultLocation}</defaultLocation> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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76 <zipOut>${jbgen.zipOut}</zipOut> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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77 <analytics>${jbgen.enableAnalytics}</analytics> |
53c2be00bb6f
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78 <primary_color>${jbgen.primary_color}</primary_color> |
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79 <secondary_color>${jbgen.secondary_color}</secondary_color> |
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80 <tertiary_color>${jbgen.tertiary_color}</tertiary_color> |
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81 <quaternary_color>${jbgen.quaternary_color}</quaternary_color> |
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82 <font_size>${jbgen.font_size}</font_size> |
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83 <session_name>${jbgen.session_name}</session_name> |
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84 </general> |
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85 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> |
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86 </metadata> |
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87 #if $jbgen.ucol.formcoll=="form": |
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88 #for $assembly in $assemblies: |
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89 <assembly> |
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90 <metadata> |
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91 <genomes> |
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92 #if str($assembly.reference_genome.genome_type_select) == "uri": |
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93 <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.refname}" useuri="yes"> |
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94 <metadata> |
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95 <dataset |
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96 dname = "${assembly.reference_genome.refname}" /> |
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97 </metadata> |
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98 </genome> |
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99 #else if str($assembly.reference_genome.genome_type_select) == "indexed": |
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100 <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.dbkey}" useuri="no"> |
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101 <metadata> |
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102 <dataset |
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103 dname = "${assembly.reference_genome.genome.fields.name}" /> |
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104 </metadata> |
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105 </genome> |
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106 #else |
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107 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no"> |
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108 <metadata> |
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109 |
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110 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}" |
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111 hid="${assembly.reference_genome.genome.hid}" |
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112 size="${assembly.reference_genome.genome.get_size(nice_size=True)}" |
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113 edam_format="${assembly.reference_genome.genome.datatype.edam_format}" |
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114 file_ext="${assembly.reference_genome.genome.ext}" |
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115 dname = "${assembly.reference_genome.genome.name}" |
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116 /> |
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117 <history |
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118 #if $assembly.reference_genome.genome.history.user: |
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119 user_email="${assembly.reference_genome.genome.history.user.email}" |
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120 user_id="${assembly.reference_genome.genome.history.user_id}" |
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121 display_name="${assembly.reference_genome.genome.history.get_display_name()}"/> |
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122 #else |
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123 user_email="anonymous" |
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124 user_id="-1" |
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125 display_name="Unnamed History" |
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126 #end if |
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127 id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}" |
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128 /> |
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129 <metadata |
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130 #for (key, value) in $assembly.reference_genome.genome.get_metadata().items(): |
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131 #if "_types" not in $key: |
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132 #if isinstance($value, list): |
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133 #set value_str = "[%s]" % ','.join([str(val) for val in value]) |
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134 ${key}="$value_str" |
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135 #else |
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136 ${key}="${value}" |
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137 #end if |
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138 #end if |
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139 #end for |
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140 /> |
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141 <tool |
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142 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}" |
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143 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}" |
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144 /> |
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145 </metadata> |
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146 </genome> |
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147 #end if |
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148 </genomes> |
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149 </metadata> |
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150 <tracks> |
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151 #for $tg in $assembly.track_groups: |
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152 #for $track in $tg.data_tracks: |
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153 #set input_exists = "False" |
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154 #if $track.data_format.useuri.insource == "uri": |
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155 #if $track.data_format.useuri.annouri: |
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156 #set input_exists = "True" |
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157 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
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158 <files> |
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159 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" |
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160 label="${track.data_format.useuri.annoname}" useuri="yes"> |
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161 <metadata> |
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162 <dataset id = "${track.data_format.useuri.annouri}" /> |
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163 </metadata> |
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164 </trackFile> |
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165 </files> |
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166 #end if |
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167 #else if $track.data_format.useuri.insource == "history": |
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168 #if $track.data_format.useuri.annotation: |
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169 #set input_exists = "True" |
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170 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
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171 <files> |
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172 #for $dataset in $track.data_format.useuri.annotation: |
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173 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no"> |
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174 <metadata> |
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175 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" |
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176 size="${dataset.get_size(nice_size=True)}" |
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177 edam_format="${dataset.datatype.edam_format}" |
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178 file_ext="${dataset.ext}" /> |
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179 <history id="${__app__.security.encode_id($dataset.history_id)}" |
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180 #if $dataset.history.user: |
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181 user_email="${dataset.history.user.email}" |
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182 user_id="${dataset.history.user_id}" |
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183 display_name="${dataset.history.get_display_name()}"/> |
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184 #else |
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185 user_email="anonymous" |
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186 user_id="-1" |
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187 display_name="Unnamed History"/> |
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188 #end if |
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189 <metadata |
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190 #for (key, value) in $dataset.get_metadata().items(): |
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191 #if "_types" not in $key and $value is not None and len(str($value)) < 5000: |
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192 #if isinstance($value, list): |
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193 #set value_str = "[%s]" % ','.join([str(val) for val in value]) |
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194 ${key}="$value_str" |
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195 #else |
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196 ${key}="${value}" |
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197 #end if |
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198 #end if |
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199 #end for |
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200 /> |
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201 <tool |
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202 tool_id="${dataset.creating_job.tool_id}" |
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203 tool_version="${dataset.creating_job.tool_version}" |
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204 /> |
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205 </metadata> |
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206 </trackFile> |
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207 #end for |
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208 </files> |
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209 #end if |
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210 #end if |
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211 #if $input_exists == "True": |
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212 <options> |
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213 <style> |
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214 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]: |
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215 <type>${track.data_format.jbstyle.display}</type> |
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216 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: |
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217 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels> |
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218 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions> |
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219 #end if |
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220 #else if str($track.data_format.data_format_select) == "vcf": |
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221 <type>${track.data_format.jbstyle.track_style.display}</type> |
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222 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: |
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223 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> |
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224 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> |
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225 #end if |
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226 |
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227 #end if |
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228 #if str($track.data_format.data_format_select) in ["bam", "cram"]: |
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229 <type>LinearAlignmentsDisplay</type> |
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230 #end if |
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231 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]: |
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232 <type>LinearHicDisplay</type> |
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233 #end if |
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234 </style> |
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235 #if str($track.data_format.data_format_select) == "bam": |
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236 <bam> |
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237 <bam_index> |
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238 #for $dataset in $track.data_format.useuri.annotation: |
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239 ${dataset} ~ ${dataset.metadata.bam_index}, |
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240 #end for |
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241 </bam_index> |
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242 </bam> |
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243 #else if str($track.data_format.data_format_select) == "cram": |
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244 <cram> |
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245 <cram_index> |
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246 #for $dataset in $track.data_format.useuri.annotation: |
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247 ${dataset} ~ ${dataset.metadata.cram_index}, |
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248 #end for |
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249 </cram_index> |
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250 </cram> |
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251 #else if str($track.data_format.data_format_select) == "blastxml": |
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252 <blast> |
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253 #if str($track.data_format.blast_parent) != "": |
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254 <parent>${track.data_format.blast_parent}</parent> |
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255 #end if |
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256 <protein>${track.data_format.is_protein}</protein> |
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257 <min_gap>${track.data_format.min_gap}</min_gap> |
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258 </blast> |
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259 #else if str($track.data_format.data_format_select) == "gff": |
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260 <gff> |
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261 #if $track.data_format.match_part.match_part_select == "true": |
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262 <match>${track.data_format.match_part.name}</match> |
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263 #end if |
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264 </gff> |
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265 #else if str($track.data_format.data_format_select) == "paf": |
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266 <paf> |
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267 #if str($track.data_format.pafuseuri.insource) == "history": |
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268 <genome> |
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269 #for $anno in $track.data_format.pafuseuri.annotation: |
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270 ${anno} ~ ${anno.name}, |
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271 #end for |
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272 </genome> |
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273 <useuri> |
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274 false |
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275 </useuri> |
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276 #else: |
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277 <genome> |
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278 #for $refgenome in $track.data_format.pafuseuri.refuri: |
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279 ${refgenome.annotation} ~ ${refgenome.annoname}, |
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280 #end for |
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281 </genome> |
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282 <useuri> |
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283 true |
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284 </useuri> |
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285 #end if |
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286 </paf> |
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287 #else if str($track.data_format.data_format_select) == "hic": |
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288 <hic> |
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289 </hic> |
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290 #else if str($track.data_format.data_format_select) == "cool": |
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291 <cool> |
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292 </cool> |
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293 #else if str($track.data_format.data_format_select) == "bed": |
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294 <bed> |
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295 </bed> |
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296 #else if str($track.data_format.data_format_select) == "sparql": |
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297 <label>${track.data_format.label}</label> |
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298 <sparql> |
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299 <url>${track.data_format.url}</url> |
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300 <query>${track.data_format.query}</query> |
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301 <query_refnames>${track.data_format.query_refnames}</query_refnames> |
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302 </sparql> |
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303 #end if |
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304 </options> |
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305 </track> |
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306 #end if |
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307 #end for |
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308 #end for |
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309 </tracks> |
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310 </assembly> |
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311 #end for |
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312 #end if |
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313 </root> |
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314 ]]></configfile> |
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315 </configfiles> |
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316 <inputs> |
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317 <repeat name="assemblies" min="1" title="Genome reference to provide display coordinates for this set of tracks" help="JBrowse2 can show a set of tracks for each of multiple genome reference fasta files"> |
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318 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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319 <param name="genome_type_select" type="select" label="Reference genome source" help="Select a built in, history or remote tabix URI for the reference track"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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320 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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321 <option value="history">Use a genome fasta file from the current history</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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322 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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323 tabix bgzip with predictable index file URI</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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324 </param> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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325 <when value="indexed"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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326 <param name="genome" type="select" optional="true" label="Select a built in reference genome or custom genome" help="If not listed, add a custom genome, use a history genome or a remote URI tabix genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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327 <options from_data_table="all_fasta"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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328 <filter column="2" type="sort_by"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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329 <validator message="No genomes are available for the selected input dataset" type="no_options"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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330 </options> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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331 </param> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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332 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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333 <when value="history"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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334 <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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335 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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336 <when value="uri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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337 <param name="uri" type="text" label="URI pointing to tabix compressed fasta"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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338 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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339 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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340 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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341 <repeat name="track_groups" title="Track Group"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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342 <param name="category" type="text" value="Default" optional="False" label="Track Category" help="Organise your tracks into Categories for a nicer end-user experience. You can use #date# and it will be replaced with the current date in 'yyyy-mm-dd' format, which is very useful for repeatedly updating a JBrowse instance when member databases / underlying tool versions are updated."/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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343 <repeat name="data_tracks" title="Annotation Track"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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344 <conditional name="data_format" label="Track Data Selection Options"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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345 <param name="data_format_select" type="select" label="Track Type"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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346 <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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347 <option value="bed">BED track</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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348 <option value="bigwig">BigWig track</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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349 <option value="blastxml">Blast XML track (as GFF3)</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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350 <option value="cram">CRAM track, we recomment to convert to BED like for BAM</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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351 <option value="gff">GFF/GFF3 track</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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352 <option value="cool">HiC as cool/mcool/scool format files</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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353 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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354 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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355 <option value="paf">PAF - approximate mapping positions between two set of sequences</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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356 <option value="vcf">VCF SNP track</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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357 </param> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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358 <when value="blastxml"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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359 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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360 <param name="blast_parent" type="data" format="gff3" optional="true" label="Features used in Blast Search" help="in GFF3. This is used so we know where to map features. E.g. where results of which CDS Protein32 match up to. The query IDs in your blast results should MATCH some feature IDs in your GFF3 file. This is an optional field and is most useful if using JBrowse to display protein blast results on a DNA genome. blastn results don't need this, blastp results on a protein sequence don't need this."/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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361 <param name="min_gap" type="integer" min="2" value="10" label="Minimum Gap Size" help="before a new match_part feature is created"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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362 <param name="is_protein" type="boolean" truevalue="true" falsevalue="false" label="Is this a protein blast search?"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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363 <expand macro="track_styling_vgp"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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364 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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365 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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366 <when value="vcf"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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367 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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368 <expand macro="track_styling_vcf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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369 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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370 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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371 <when value="gff"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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372 <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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373 <conditional name="match_part" label="match/match_part data"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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374 <param name="match_part_select" type="select" label="This is match/match_part data" help="Match part data selection "> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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375 <option selected="True" value="false">Not match/match part data</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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376 <option value="true">Match/match part data</option> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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377 </param> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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378 <when value="true"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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379 <param name="name" type="text" value="match" optional="True" label="Match Part Feature Type" help="Match_parts have options for the parent feature type, such as cDNA_match, match, translated_nucleotide_match, etc. Please select the appropriate one here. You can leave empty to try autodetection (only works with CanvasFeatures track type)."/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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380 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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381 <when value="false"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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382 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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383 <expand macro="track_styling_vgp"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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384 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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385 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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386 <when value="bam"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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387 <expand macro="input_conditional" label="BAM Track Data" format="bam"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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388 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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389 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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390 <when value="bed"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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391 <expand macro="input_conditional" label="BED Track Data" format="bed"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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392 <expand macro="track_styling_vgp"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
393 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
394 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
395 <when value="cram"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
396 <expand macro="input_conditional" label="CRAM Track Data" format="cram"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
397 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
398 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
399 <when value="maf"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
400 <expand macro="input_conditional" label="MAF Track Data" format="maf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
401 <expand macro="track_styling_vgp"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
402 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
403 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
404 <when value="bigwig"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
405 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
406 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
407 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
408 <when value="paf"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
409 <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf" help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
410 <expand macro="pafref_conditional" label="Comparison genome sequence(s)" format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
411 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
412 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
413 <when value="hic"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
414 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
415 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
416 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
417 <when value="cool"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
418 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
419 <expand macro="track_visibility"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
420 </when> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
421 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
422 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
423 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
424 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
425 <expand macro="general_options"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
426 </inputs> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
427 <outputs> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
428 <data format="html" name="output" label="JBrowse2: ${jbgen.session_name}"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
429 <change_format> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
430 <when input="zipOut" value="true" format="zip"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
431 </change_format> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
432 </data> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
433 </outputs> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
434 <tests> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
435 <test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
436 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
437 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
438 <param name="genome_type_select" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
439 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Merlin"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
440 <param name="genome.ext" value="fasta"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
441 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
442 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
443 <param name="category" value="Assembly properties"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
444 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
445 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
446 <param name="data_format_select" value="gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
447 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
448 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
449 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.gff3"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
450 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
451 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
452 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
453 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
454 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
455 <param name="data_format_select" value="bigwig"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
456 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
457 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
458 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.bw"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
459 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
460 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
461 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
462 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
463 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
464 <param name="data_format_select" value="bed"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
465 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
466 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
467 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/test-6.bed"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
468 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
469 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
470 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
471 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
472 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
473 <param name="data_format_select" value="vcf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
474 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
475 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
476 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.vcf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
477 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
478 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
479 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
480 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
481 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
482 <param name="data_format_select" value="cram"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
483 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
484 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
485 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.cram"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
486 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
487 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
488 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
489 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
490 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
491 <param name="data_format_select" value="bam"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
492 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
493 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
494 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin-sample.bam"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
495 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
496 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
497 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
498 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
499 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
500 <param name="data_format_select" value="maf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
501 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
502 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
503 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlinlastz.maf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
504 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
505 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
506 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
507 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
508 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
509 <param name="data_format_select" value="blastxml"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
510 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
511 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
512 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.blastxml"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
513 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
514 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
515 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
516 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
517 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
518 <param name="data_format_select" value="bam"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
519 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
520 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
521 <param name="annotation" value=""/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
522 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
523 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
524 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
525 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
526 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
527 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
528 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
529 <param name="genome_type_select" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
530 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
531 <param name="genome.ext" value="fasta"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
532 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
533 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
534 <param name="category" value="Assembly properties"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
535 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
536 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
537 <param name="data_format_select" value="cool"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
538 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
539 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
540 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3test.cool"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
541 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
542 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
543 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
544 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
545 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
546 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
547 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
548 <param name="genome_type_select" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
549 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Ppersica1.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
550 <param name="genome.ext" value="fasta"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
551 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
552 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
553 <param name="category" value="Assembly properties"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
554 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
555 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
556 <param name="data_format_select" value="paf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
557 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
558 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
559 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/peach-grape-map.paf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
560 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
561 <conditional name="pafuseuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
562 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
563 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
564 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
565 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
566 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
567 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
568 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
569 <param name="data_format_select" value="paf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
570 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
571 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
572 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
573 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
574 <conditional name="pafuseuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
575 <param name="insource" value="uri"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
576 <repeat name="refuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
577 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
578 <param name="annoname" value="arabidopsis.URI"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
579 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
580 <repeat name="refuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
581 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
582 <param name="annoname" value="Vvinifera1.URI"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
583 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
584 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
585 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
586 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
587 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
588 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
589 <param name="data_format_select" value="paf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
590 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
591 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
592 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
593 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
594 <conditional name="pafuseuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
595 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
596 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
597 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
598 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
599 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
600 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
601 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
602 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
603 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
604 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
605 <param name="genome_type_select" value="uri"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
606 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
607 <param name="refname" value="hg38"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
608 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
609 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
610 <param name="category" value="Assembly properties"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
611 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
612 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
613 <param name="data_format_select" value="hic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
614 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
615 <param name="insource" value="uri"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
616 <param name="annouri" value="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
617 <param name="annoname" value="humanhic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
618 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
619 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
620 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
621 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
622 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
623 <section name="jbgen"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
624 <param name="zipOut" value="true"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
625 <param name="session_name" value="New test session"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
626 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
627 <!-- use the following line to generate a ZIP file to inspect it --> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
628 <!--output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"--> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
629 <output name="output" ftype="zip"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
630 <assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
631 <has_archive_member path=".*" n="637" delta="10"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
632 <has_archive_member path="index.html"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
633 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
634 <has_archive_member path="manifest.json"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
635 <has_text text="favicon.ico"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
636 <has_text text="background_color"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
637 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
638 <has_archive_member path="galaxy.xml"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
639 <is_valid_xml/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
640 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
641 <element_text_is path="./metadata/general/session_name" text="New test session"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
642 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
643 <has_archive_member path="merlin.gff3_0.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
644 <has_archive_member path="merlin.gff3_0.gz.tbi"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
645 <has_archive_member path="merlin.bw_1"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
646 <has_archive_member path="test-6.bed_2.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
647 <has_archive_member path="merlin.vcf_3"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
648 <has_archive_member path="merlin.vcf_3.tbi"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
649 <has_archive_member path="merlin.cram_4"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
650 <has_archive_member path="merlin.cram_4.crai"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
651 <has_archive_member path="merlin-sample.bam_5"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
652 <has_archive_member path="merlin-sample.bam_5.bai"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
653 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
654 <has_archive_member path="merlin.blastxml_7.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
655 <has_archive_member path="dm3test.cool_9.hic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
656 <has_archive_member path="peach-grape-map.paf_10"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
657 <has_archive_member path="arabgrapepeach.paf_11"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
658 <has_archive_member path="Merlin.fa.gz.fai"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
659 <has_archive_member path="dm3.fa.fa.gz.fai"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
660 <has_archive_member path="Ppersica1.fa.fa.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
661 <has_archive_member path="Ppersica1.fa.fa.gz.fai"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
662 <has_archive_member path="Ppersica1.fa.fa.gz.gzi"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
663 <has_archive_member path="Vvinifera1.fa.fa.gz.fai"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
664 <has_archive_member path="Vvinifera1.fa.fa.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
665 <has_archive_member path="Vvinifera1.fa.fa.gz.gzi"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
666 <has_archive_member path="config.json"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
667 <has_json_property_with_text property="name" text="Merlin"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
668 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
669 </assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
670 </output> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
671 </test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
672 <test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
673 <param name="autoCollection"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
674 <collection type="list" name="merlintest"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
675 <element name="merlin.fa" value="merlin.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
676 <element name="merlin.bw" value="bw/merlin.bw"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
677 <element name="test-6.bed" value="bed/test-6.bed"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
678 </collection> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
679 </param> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
680 <section name="jbgen"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
681 <param name="zipOut" value="true"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
682 <param name="session_name" value="Collection test"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
683 <param name="ucol|formcoll" value="collect"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
684 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
685 <!-- use the following line to generate a ZIP file to inspect it --> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
686 <!--output name="output" file="jbrowse2_result01.zip" ftype="zip" compare="sim_size"--> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
687 <output name="output" ftype="zip"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
688 <assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
689 <has_archive_member path=".*" n="611" delta="10"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
690 <has_archive_member path="index.html"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
691 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
692 <has_archive_member path="manifest.json"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
693 <has_text text="favicon.ico"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
694 <has_text text="background_color"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
695 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
696 <has_archive_member path="galaxy.xml"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
697 <is_valid_xml/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
698 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
699 <element_text_is path="./metadata/general/session_name" text="Collection test"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
700 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
701 <has_archive_member path="jb2_webserver.py"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
702 <has_archive_member path="merlin.fa.fa.gz.gzi"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
703 <has_archive_member path="merlin.fa.fa.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
704 <has_archive_member path="merlin.fa.fa.gz.fai"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
705 <has_archive_member path="merlin.bw"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
706 <has_archive_member path="index.html"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
707 <has_archive_member path="test-6.bed.gz"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
708 <has_archive_member path="test-6.bed.gz.tbi"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
709 </assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
710 </output> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
711 </test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
712 <test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
713 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
714 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
715 <param name="genome_type_select" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
716 <param name="genome" value="merlin.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
717 <param name="genome.ext" value="fasta"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
718 <param name="genome.name" value="Merlin"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
719 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
720 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
721 <param name="category" value="Default"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
722 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
723 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
724 <param name="data_format_select" value="bigwig"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
725 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
726 <param name="annotation" value="bw/merlin.bw"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
727 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
728 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
729 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
730 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
731 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
732 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
733 <section name="jbgen"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
734 <param name="zipOut" value="true"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
735 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
736 <output name="output"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
737 <assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
738 <has_archive_member path="galaxy.xml"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
739 <has_text text="genome path="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
740 <has_text text="label="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
741 <has_text text="format="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
742 <has_text text="metadata"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
743 <has_text text="useuri="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
744 <has_text text="trackFile path="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
745 <has_text text="ext="bigwig""/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
746 <has_text text="format="bigwig""/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
747 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
748 </assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
749 </output> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
750 </test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
751 <test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
752 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
753 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
754 <param name="genome_type_select" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
755 <param name="genome" value="merlin.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
756 <param name="genome.ext" value="fasta"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
757 <param name="genome.name" value="Merlin"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
758 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
759 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
760 <param name="category" value="Default"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
761 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
762 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
763 <param name="data_format_select" value="vcf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
764 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
765 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
766 <param name="annotation" value="vcf/merlin.vcf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
767 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
768 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
769 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
770 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
771 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
772 <section name="jbgen"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
773 <param name="zipOut" value="true"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
774 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
775 <output name="output"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
776 <assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
777 <has_archive_member path="galaxy.xml"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
778 <has_text text="genome path="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
779 <has_text text="label="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
780 <has_text text="format="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
781 <has_text text="metadata"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
782 <has_text text="useuri="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
783 <has_text text="trackFile path="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
784 <has_text text="ext="vcf" label="merlin.vcf""/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
785 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
786 </assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
787 </output> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
788 </test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
789 <test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
790 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
791 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
792 <param name="genome_type_select" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
793 <param name="genome" value="merlin.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
794 <param name="genome.ext" value="fasta"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
795 <param name="genome.name" value="Merlin"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
796 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
797 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
798 <section name="jbgen"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
799 <param name="zipOut" value="true"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
800 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
801 <output name="output"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
802 <assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
803 <has_archive_member path="galaxy.xml"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
804 <has_text text="genome path="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
805 <has_text text="label="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
806 <has_text text="useuri="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
807 <has_text text="metadata"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
808 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
809 </assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
810 </output> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
811 </test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
812 <test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
813 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
814 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
815 <param name="genome_type_select" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
816 <param name="genome" value="merlin.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
817 <param name="genome.ext" value="fasta"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
818 <param name="genome.name" value="Merlin"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
819 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
820 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
821 <param name="category" value="Default"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
822 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
823 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
824 <param name="data_format_select" value="vcf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
825 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
826 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
827 <param name="annotation" value="vcf/merlin.vcf"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
828 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
829 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
830 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
831 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
832 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
833 <section name="jbgen"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
834 <param name="zipOut" value="true"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
835 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
836 <output name="output"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
837 <assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
838 <has_archive_member path="galaxy.xml"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
839 <has_text text="genome path="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
840 <has_text text="label="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
841 <has_text text="format="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
842 <has_text text="metadata"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
843 <has_text text="useuri="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
844 <has_text text="trackFile path="/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
845 <has_text text="ext="vcf" label="merlin.vcf""/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
846 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
847 </assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
848 </output> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
849 </test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
850 <test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
851 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
852 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
853 <param name="genome_type_select" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
854 <param name="genome" value="merlin.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
855 <param name="genome.ext" value="fasta"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
856 <param name="genome.name" value="Merlin"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
857 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
858 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
859 <param name="category" value="Default"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
860 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
861 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
862 <param name="data_format_select" value="gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
863 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
864 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
865 <param name="annotation" value="gff3/A.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
866 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
867 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
868 <conditional name="match_part"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
869 <param name="match_part_select" value="false"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
870 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
871 <section name="jbcolor_scale"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
872 <conditional name="color_score"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
873 <param name="color_score_select" value="none"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
874 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
875 <conditional name="color"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
876 <param name="color_select" value="automatic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
877 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
878 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
879 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
880 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
881 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
882 <param name="category" value="Ignore Scale"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
883 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
884 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
885 <param name="data_format_select" value="gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
886 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
887 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
888 <param name="annotation" value="gff3/1.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
889 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
890 <conditional name="match_part"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
891 <param name="match_part_select" value="false"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
892 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
893 <section name="jbcolor_scale"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
894 <conditional name="color_score"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
895 <param name="color_score_select" value="none"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
896 <conditional name="color"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
897 <param name="color_select" value="manual"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
898 <param name="style_color" value="#ff00ff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
899 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
900 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
901 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
902 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
903 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
904 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
905 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
906 <param name="category" value="Scaled Colour"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
907 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
908 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
909 <param name="data_format_select" value="gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
910 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
911 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
912 <param name="annotation" value="gff3/C.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
913 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
914 <conditional name="match_part"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
915 <param name="match_part_select" value="false"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
916 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
917 <section name="jbcolor_scale"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
918 <conditional name="color_score"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
919 <param name="color_score_select" value="score"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
920 <param name="score_scaling" value="linear"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
921 <conditional name="score_scales"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
922 <param name="scale_select" value="automatic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
923 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
924 <conditional name="color_scheme"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
925 <param name="score_scheme" value="opacity"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
926 <conditional name="color"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
927 <param name="color_select" value="automatic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
928 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
929 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
930 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
931 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
932 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
933 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
934 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
935 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
936 <param name="data_format_select" value="gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
937 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
938 <param name="annotation" value="gff3/B.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
939 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
940 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
941 <conditional name="match_part"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
942 <param name="match_part_select" value="false"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
943 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
944 <section name="jbcolor_scale"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
945 <conditional name="color_score"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
946 <param name="color_score_select" value="score"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
947 <param name="score_scaling" value="linear"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
948 <conditional name="score_scales"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
949 <param name="scale_select" value="automatic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
950 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
951 <conditional name="color_scheme"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
952 <param name="score_scheme" value="opacity"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
953 <conditional name="color"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
954 <param name="color_select" value="manual"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
955 <param name="style_color" value="#0000ff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
956 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
957 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
958 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
959 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
960 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
961 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
962 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
963 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
964 <param name="data_format_select" value="gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
965 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
966 <param name="annotation" value="gff3/A.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
967 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
968 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
969 <conditional name="match_part"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
970 <param name="match_part_select" value="false"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
971 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
972 <section name="jbcolor_scale"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
973 <conditional name="color_score"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
974 <param name="color_score_select" value="score"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
975 <param name="score_scaling" value="linear"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
976 <conditional name="score_scales"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
977 <param name="scale_select" value="manual"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
978 <param name="minimum" value="0"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
979 <param name="maximum" value="1000"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
980 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
981 <conditional name="color_scheme"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
982 <param name="score_scheme" value="opacity"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
983 <conditional name="color"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
984 <param name="color_select" value="automatic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
985 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
986 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
987 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
988 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
989 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
990 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
991 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
992 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
993 <param name="data_format_select" value="gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
994 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
995 <param name="annotation" value="gff3/1.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
996 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
997 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
998 <conditional name="match_part"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
999 <param name="match_part_select" value="false"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1000 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1001 <section name="jbcolor_scale"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1002 <conditional name="color_score"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1003 <param name="color_score_select" value="score"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1004 <param name="score_scaling" value="linear"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1005 <conditional name="score_scales"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1006 <param name="scale_select" value="manual"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1007 <param name="minimum" value="0"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1008 <param name="maximum" value="1000"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1009 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1010 <conditional name="color_scheme"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1011 <param name="score_scheme" value="opacity"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1012 <conditional name="color"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1013 <param name="color_select" value="manual"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1014 <param name="style_color" value="#ff0000"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1015 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1016 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1017 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1018 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1019 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1020 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1021 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1022 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1023 <param name="category" value="Realistic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1024 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1025 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1026 <param name="data_format_select" value="gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1027 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1028 <param name="annotation" value="gff3/interpro.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1029 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1030 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1031 <conditional name="match_part"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1032 <param name="match_part_select" value="false"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1033 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1034 <section name="jbcolor_scale"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1035 <conditional name="color_score"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1036 <param name="color_score_select" value="none"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1037 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1038 <conditional name="color"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1039 <param name="color_select" value="automatic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1040 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1041 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1042 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1043 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1044 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1045 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1046 <param name="data_format_select" value="gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1047 <conditional name="useuri"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1048 <param name="annotation" value="gff3/2.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1049 <param name="insource" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1050 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1051 <conditional name="match_part"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1052 <param name="match_part_select" value="true"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1053 <param name="name" value="cDNA_match"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1054 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1055 <section name="jbcolor_scale"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1056 <conditional name="color_score"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1057 <param name="color_score_select" value="none"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1058 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1059 <conditional name="color"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1060 <param name="color_select" value="automatic"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1061 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1062 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1063 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1064 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1065 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1066 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1067 <section name="jbgen"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1068 <param name="zipOut" value="true"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1069 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1070 <output name="output"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1071 <assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1072 <has_archive_member path="A.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1073 <has_archive_member path="B.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1074 <has_archive_member path="C.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1075 <has_archive_member path="interpro.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1076 <has_archive_member path="1.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1077 <has_archive_member path="2.gff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1078 <has_archive_member path="galaxy.xml"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1079 <is_valid_xml/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1080 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1081 <element_text_is path="./metadata/general/session_name" text="New JBrowse2 session"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1082 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1083 </assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1084 </output> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1085 </test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1086 <test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1087 <repeat name="assemblies"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1088 <conditional name="reference_genome"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1089 <param name="genome_type_select" value="history"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1090 <param name="genome" value="merlin.fa"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1091 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1092 <repeat name="track_groups"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1093 <param name="category" value="Auto Coloured"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1094 <repeat name="data_tracks"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1095 <conditional name="data_format"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1096 <param name="data_format_select" value="cram"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1097 <param name="annotation" value="cram/merlin-sample.cram"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1098 </conditional> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1099 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1100 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1101 </repeat> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1102 <section name="jbgen"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1103 <param name="zipOut" value="true"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1104 </section> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1105 <output name="output" ftype="zip"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1106 <assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1107 <!-- roughly 590 files in an archive --> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1108 <has_archive_member path=".*" n="608" delta="30"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1109 <has_archive_member path="index.html"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1110 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1111 <has_archive_member path="manifest.json"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1112 <has_text text="favicon.ico"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1113 <has_text text="background_color"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1114 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1115 <has_archive_member path="merlin.fa.fa.gz.fai"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1116 <has_archive_member path="galaxy.xml"> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1117 <is_valid_xml/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1118 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
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changeset
|
1119 <element_text_is path="./metadata/general/session_name" text="New JBrowse2 session"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1120 </has_archive_member> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1121 </assert_contents> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1122 </output> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1123 </test> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1124 </tests> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
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changeset
|
1125 <help><![CDATA[ |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1126 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1127 JBrowse2-in-Galaxy |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1128 ================== |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1129 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1130 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible Genome viewer. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1131 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1132 Compared to JBrowse1-in-Galaxy, there is no support for alternative codons for unusual genomes, |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1133 and detailed track styling is not yet implemented. Please contact us if you are missing features. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1134 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1135 Use and local viewing |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1136 ===================== |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1137 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1138 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1139 A JBrowse2 history item can be opened by viewing it (the "eye" icon). |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1140 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1141 The same browser data and setup can also be downloaded as a compressed zip archive by clicking the download ("floppy disk") icon in the history. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1142 This can be shared and viewed without Galaxy. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1143 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1144 A replacement application to serve the browser is required without Galaxy. A local python web server can be started using a script included in each archive, |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1145 assuming that Python3 is already working on your desktop - if not you will have to install it first. Unzip the archive (*unzip [filename].zip*) and change |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
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|
1146 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py* |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
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changeset
|
1147 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1148 With python3 installed, |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1149 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1150 *python3 jb2_webserver.py* |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1151 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1152 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open, |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1153 but the script appears to be running, try pointing your web browser to the default of *localhost:8080* |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
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changeset
|
1154 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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diff
changeset
|
1155 Overview |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
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|
1156 -------- |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1157 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1158 JBrowse is a fast, embeddable genome browser built completely with |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1159 JavaScript and HTML5. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
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|
1160 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
bgruening
parents:
diff
changeset
|
1161 The JBrowse-in-Galaxy (JiG) tool was written to help build complex |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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parents:
diff
changeset
|
1162 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1163 about how to run the command line tools to format your data, and which |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1164 options need to be supplied and where. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1165 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1166 Options |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1167 ------- |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1168 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1169 **Reference or Assembly** |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1170 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1171 Choose either a built-in or select one from your history. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1172 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1173 Track coordinates and contig names *must* match this reference precisely |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1174 or they will not display. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1175 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1176 **Track Groups** represent a set of tracks in a single category. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1177 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1178 Annotation Tracks |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1179 ----------------- |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1180 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1181 MAF |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1182 ~~~ |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1183 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1184 For history references, the name of the reference genome dataset in your history is very important for MAF tracks, |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1185 because it becomes the "dbkey" for that reference. So, it must be exactly the same as the genome name (dbkey) used |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1186 when making the MAF, typically in the Lastz tool. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1187 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1188 If you used "hg38" as the reference in Lastz, that is exactly what the reference fasta should be named for any MAF track. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1189 Change it using the "pencil" icon on the reference data in your history. Any other name, such as "hg38.fasta" |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1190 will cause the MAF track to show no data since there are no matches with that reference dbkey. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1191 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1192 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1193 GFF3/BED |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1194 ~~~~~~~~ |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1195 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1196 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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changeset
|
1197 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1198 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1199 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1200 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1201 well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1202 lengths of each assembly or reference contig. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1203 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1204 BAM Pileups |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1205 ~~~~~~~~~~~ |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1206 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1207 We support BAM files and can automatically generate SNP tracks based on |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1208 that bam data. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1209 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1210 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1211 BlastXML |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1212 ~~~~~~~~ |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1213 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1214 JiG now supports both blastn and blastp datasets. JiG internally uses a |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1215 blastXML to gapped GFF3 tool to convert your blastxml datasets into a |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1216 format amenable to visualization in JBrowse. This tool is also |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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|
1217 available separately from the IUC on the toolshed. |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1218 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1219 **Minimum Gap Size** reflects how long a gap must be before it becomes a |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1220 real gap in the processed gff3 file. In the picture above, various sizes |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1221 of gaps can be seen. If the minimum gap size was set much higher, say |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1222 100nt, many of the smaller gaps would disappear, and the features on |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1223 both sides would be merged into one, longer feature. This setting is |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1224 inversely proportional to runtime and output file size. *Do not set this |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1225 to a low value for large datasets*. By setting this number lower, you |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1226 will have extremely large outputs and extremely long runtimes. The |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1227 default was configured based off of the author's experience, but the |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1228 author only works on small viruses. It is *strongly* recommended that |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1229 you filter your blast results before display, e.g. picking out the top |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1230 10 hits or so. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1231 |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1232 **Protein blast search** option merely informs underlying tools that |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1233 they should adjust feature locations by 3x. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1234 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1235 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1236 ]]></help> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1237 <expand macro="citations"/> |
53c2be00bb6f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1238 <expand macro="creators"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0a86c88a95b0d1cc49d84544136de6556b95320f
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1239 </tool> |