Mercurial > repos > fubar > jbrowse2
annotate jbrowse2.xml @ 113:878c27dfea9d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0
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date | Sun, 28 Jul 2024 02:42:43 +0000 |
parents | 56f9a6e0fe80 |
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b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1 <tool id="jbrowse2" name="JBrowse2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05"> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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2 <description>genome browser</description> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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3 <macros> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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4 <import>macros.xml</import> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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5 </macros> |
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74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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6 <expand macro="edamInc"/> |
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d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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7 <xrefs> |
113
878c27dfea9d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0
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8 <xref type="bio.tools">jbrowse_2</xref> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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9 </xrefs> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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10 <expand macro="requirements"/> |
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74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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11 <required_files> |
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b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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12 <include path="autogenJB2.py"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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13 <include path="blastxml_to_gapped_gff3.py"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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14 <include path="convertMAF.sh"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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15 <include path="gff3_rebase.py"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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16 <include path="jb2_webserver.py"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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17 <include path="jbrowse2.py"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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18 <include path="maf2bed.py"/> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
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19 </required_files> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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20 <version_command>python '${__tool_directory__}/jbrowse2.py' --version</version_command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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21 <command detect_errors="aggressive"><![CDATA[ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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22 mkdir -p '$output.files_path' && |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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23 cp '$trackxml' '$output.files_path/galaxy.xml' && |
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b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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24 export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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25 #if $jbgen.ucol.formcoll=="collect": |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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26 python '$__tool_directory__/autogenJB2.py' |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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27 #for $key in $autoCollection.keys(): |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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28 #if $autoCollection[$key].is_collection: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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29 #set subCol=$autoCollection[$key] |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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30 #set pafs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext == 'paf'] |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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31 #set refs=[($subCol[x],$subcol[x].ext,x) for x in $subCol.keys() if $subCol[x].ext in ['fasta.gz','fasta']] |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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32 #if len($pafs) > 0: |
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b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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33 --pafmeta '$pafs[0]' |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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34 #for $ref in $refs: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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35 --pafreferencemeta '$ref' |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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36 #end for |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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37 #end if |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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38 #else if $autoCollection[$key].ext == 'fasta': |
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b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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39 --referencemeta '$autoCollection[$key],$autoCollection[$key].ext,$key' |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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40 #else if $autoCollection[$key].ext in ['bed', 'bigwig', 'cool', 'gff', 'gff3', 'hic', 'maf', 'mcool', 'scool', 'vcf'] |
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b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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41 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key' |
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4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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42 #else if $autoCollection[$key].ext in ['bam',] |
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b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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43 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.bam_index' |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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44 #else if $autoCollection[$key].ext in ['cram',] |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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45 --trackmeta '$autoCollection[$key],$autoCollection[$key].ext,$key,$autoCollection[$key].metadata.cram_index' |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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46 #end if |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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47 #end for |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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48 --outdir '$output.files_path' |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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49 --jbrowse2path \${JBROWSE2_PATH} |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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50 --sessName "Autogen JBrowse" && |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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51 #if $jbgen.zipOut == "true": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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52 cd '$output.files_path' && |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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53 zip -r - . > '$output' |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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54 #else |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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55 cp '$output.files_path/index.html' '$output' |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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56 #end if |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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57 #else: |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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58 python '$__tool_directory__/jbrowse2.py' |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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59 --jbrowse2path \${JBROWSE2_PATH} |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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60 --outdir '$output.files_path' |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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61 --xml '$trackxml' && |
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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62 #if $jbgen.zipOut == "true": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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63 cd '$output.files_path' && |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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64 zip -r - . > '$output' |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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65 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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66 cp '$output.files_path/index.html' '$output' |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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67 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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68 #end if |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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69 ]]></command> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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70 <configfiles> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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71 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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72 <root> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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73 <metadata> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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74 <general> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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75 <defaultLocation>${jbgen.defaultLocation}</defaultLocation> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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76 <zipOut>${jbgen.zipOut}</zipOut> |
101
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77 <bpPerPx>${jbgen.bpPerPx}</bpPerPx> |
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78 <analytics>${jbgen.enableAnalytics}</analytics> |
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79 <primary_color>${jbgen.primary_color}</primary_color> |
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80 <secondary_color>${jbgen.secondary_color}</secondary_color> |
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81 <tertiary_color>${jbgen.tertiary_color}</tertiary_color> |
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82 <quaternary_color>${jbgen.quaternary_color}</quaternary_color> |
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83 <font_size>${jbgen.font_size}</font_size> |
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84 <session_name>${jbgen.session_name}</session_name> |
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85 </general> |
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86 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> |
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87 </metadata> |
62
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88 #if $jbgen.ucol.formcoll=="form": |
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89 #for $assembly in $assemblies: |
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90 <assembly> |
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91 <metadata> |
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92 <genomes> |
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93 #if str($assembly.reference_genome.genome_type_select) == "uri": |
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94 <genome path="${assembly.reference_genome.uri}" label="${assembly.reference_genome.refname}" useuri="yes"> |
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95 <metadata> |
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96 <dataset |
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97 dname = "${assembly.reference_genome.refname}" /> |
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98 </metadata> |
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99 </genome> |
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100 #else if str($assembly.reference_genome.genome_type_select) == "indexed": |
87
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101 <genome path="${assembly.reference_genome.genome.fields.path}" label="${assembly.reference_genome.genome.fields.dbkey}" useuri="no"> |
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102 <metadata> |
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103 <dataset |
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104 dname = "${assembly.reference_genome.genome.fields.name}" /> |
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105 </metadata> |
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106 </genome> |
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107 #else |
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108 <genome path="$assembly.reference_genome.genome" label="${assembly.reference_genome.genome.name}" useuri="no"> |
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109 <metadata> |
88
efd1d41f11b4
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110 |
62
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111 <dataset id="${__app__.security.encode_id($assembly.reference_genome.genome.id)}" |
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112 hid="${assembly.reference_genome.genome.hid}" |
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113 size="${assembly.reference_genome.genome.get_size(nice_size=True)}" |
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114 edam_format="${assembly.reference_genome.genome.datatype.edam_format}" |
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115 file_ext="${assembly.reference_genome.genome.ext}" |
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116 dname = "${assembly.reference_genome.genome.name}" |
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117 /> |
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118 <history |
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119 #if $assembly.reference_genome.genome.history.user: |
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120 user_email="${assembly.reference_genome.genome.history.user.email}" |
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121 user_id="${assembly.reference_genome.genome.history.user_id}" |
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122 display_name="${assembly.reference_genome.genome.history.get_display_name()}"/> |
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123 #else |
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124 user_email="anonymous" |
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125 user_id="-1" |
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126 display_name="Unnamed History" |
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127 #end if |
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128 id="${__app__.security.encode_id($assembly.reference_genome.genome.history_id)}" |
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129 /> |
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130 <metadata |
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131 #for (key, value) in $assembly.reference_genome.genome.get_metadata().items(): |
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132 #if "_types" not in $key: |
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133 #if isinstance($value, list): |
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134 #set value_str = "[%s]" % ','.join([str(val) for val in value]) |
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135 ${key}="$value_str" |
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136 #else |
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137 ${key}="${value}" |
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138 #end if |
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139 #end if |
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140 #end for |
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141 /> |
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142 <tool |
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143 tool_id="${assembly.reference_genome.genome.creating_job.tool_id}" |
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144 tool_version="${assembly.reference_genome.genome.creating_job.tool_version}" |
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145 /> |
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146 </metadata> |
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147 </genome> |
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148 #end if |
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149 </genomes> |
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150 </metadata> |
0
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151 <tracks> |
62
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152 #for $tg in $assembly.track_groups: |
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153 #for $track in $tg.data_tracks: |
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154 #set input_exists = "False" |
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155 #if $track.data_format.useuri.insource == "uri": |
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156 #if $track.data_format.useuri.annouri: |
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157 #set input_exists = "True" |
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158 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
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159 <files> |
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160 <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" |
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161 label="${track.data_format.useuri.annoname}" useuri="yes"> |
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162 <metadata> |
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163 <dataset id = "${track.data_format.useuri.annouri}" /> |
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164 </metadata> |
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165 </trackFile> |
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166 </files> |
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167 #end if |
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168 #else if $track.data_format.useuri.insource == "history": |
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169 #if $track.data_format.useuri.annotation: |
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170 #set input_exists = "True" |
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171 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
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172 <files> |
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173 #for $dataset in $track.data_format.useuri.annotation: |
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174 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.name}" useuri="no"> |
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175 <metadata> |
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176 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" |
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177 size="${dataset.get_size(nice_size=True)}" |
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178 edam_format="${dataset.datatype.edam_format}" |
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179 file_ext="${dataset.ext}" /> |
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180 <history id="${__app__.security.encode_id($dataset.history_id)}" |
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181 #if $dataset.history.user: |
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182 user_email="${dataset.history.user.email}" |
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183 user_id="${dataset.history.user_id}" |
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184 display_name="${dataset.history.get_display_name()}"/> |
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185 #else |
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186 user_email="anonymous" |
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187 user_id="-1" |
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188 display_name="Unnamed History"/> |
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189 #end if |
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190 <metadata |
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191 #for (key, value) in $dataset.get_metadata().items(): |
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192 #if "_types" not in $key and $value is not None and len(str($value)) < 5000: |
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193 #if isinstance($value, list): |
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194 #set value_str = "[%s]" % ','.join([str(val) for val in value]) |
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195 ${key}="$value_str" |
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196 #else |
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197 ${key}="${value}" |
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198 #end if |
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199 #end if |
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200 #end for |
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201 /> |
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202 <tool |
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203 tool_id="${dataset.creating_job.tool_id}" |
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204 tool_version="${dataset.creating_job.tool_version}" |
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205 /> |
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206 </metadata> |
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207 </trackFile> |
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208 #end for |
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209 </files> |
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210 #end if |
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211 #end if |
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212 #if $input_exists == "True": |
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213 <options> |
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214 <style> |
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215 #if str($track.data_format.data_format_select) in ["gff", "bed", "maf", "blastxml"]: |
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216 <type>${track.data_format.jbstyle.display}</type> |
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217 #if str($track.data_format.jbstyle.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: |
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218 <trackShowLabels>${track.data_format.jbstyle.show_labels}</trackShowLabels> |
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219 <trackShowDescriptions>${track.data_format.jbstyle.show_descriptions}</trackShowDescriptions> |
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220 #end if |
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221 #else if str($track.data_format.data_format_select) == "vcf": |
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222 <type>${track.data_format.jbstyle.track_style.display}</type> |
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223 #if str($track.data_format.jbstyle.track_style.display) in ["LinearBasicDisplay", "LinearVariantDisplay"]: |
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224 <trackShowLabels>${track.data_format.jbstyle.track_style.show_labels}</trackShowLabels> |
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225 <trackShowDescriptions>${track.data_format.jbstyle.track_style.show_descriptions}</trackShowDescriptions> |
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226 #end if |
103
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227 #else if str($track.data_format.data_format_select) == "bigwig": |
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228 <type>${track.data_format.jbstyle.track_style.display}</type> |
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229 <color>${track.data_format.jbstyle.track_style.color}</color> |
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230 <autoscale>${track.data_format.jbstyle.track_style.autoscale}</autoscale> |
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231 <resolution>${track.data_format.jbstyle.track_style.resolution}</resolution> |
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232 <summaryScoreMode>${track.data_format.jbstyle.track_style.summaryScoreMode}</summaryScoreMode> |
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233 <filled>${track.data_format.jbstyle.track_style.filled}</filled> |
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234 <scaleType>${track.data_format.jbstyle.track_style.scaleType}</scaleType> |
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235 <displayCrossHatches>${track.data_format.jbstyle.track_style.displayCrossHatches}</displayCrossHatches> |
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236 <minScore>${track.data_format.jbstyle.track_style.minScore}</minScore> |
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237 <maxScore>${track.data_format.jbstyle.track_style.maxScore}</maxScore> |
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238 #end if |
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239 #if str($track.data_format.data_format_select) in ["bam", "cram"]: |
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240 <type>LinearAlignmentsDisplay</type> |
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241 #end if |
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242 #if str($track.data_format.data_format_select) in ["hic", "cool", "mcool", "scool"]: |
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243 <type>LinearHicDisplay</type> |
85
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244 #end if |
88
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245 </style> |
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246 #if str($track.data_format.data_format_select) == "bam": |
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247 <bam> |
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248 <bam_index> |
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249 #for $dataset in $track.data_format.useuri.annotation: |
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250 ${dataset} ~ ${dataset.metadata.bam_index}, |
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251 #end for |
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252 </bam_index> |
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253 </bam> |
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254 #else if str($track.data_format.data_format_select) == "cram": |
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255 <cram> |
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256 <cram_index> |
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257 #for $dataset in $track.data_format.useuri.annotation: |
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258 ${dataset} ~ ${dataset.metadata.cram_index}, |
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259 #end for |
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260 </cram_index> |
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261 </cram> |
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262 #else if str($track.data_format.data_format_select) == "blastxml": |
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263 <blast> |
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264 #if str($track.data_format.blast_parent) != "": |
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265 <parent>${track.data_format.blast_parent}</parent> |
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266 #end if |
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267 <protein>${track.data_format.is_protein}</protein> |
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268 <min_gap>${track.data_format.min_gap}</min_gap> |
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269 </blast> |
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270 #else if str($track.data_format.data_format_select) == "gff": |
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271 <gff> |
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272 #if $track.data_format.match_part.match_part_select == "true": |
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273 <match>${track.data_format.match_part.name}</match> |
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274 #end if |
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275 </gff> |
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276 #else if str($track.data_format.data_format_select) == "paf": |
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277 <paf> |
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278 #if str($track.data_format.pafuseuri.insource) == "history": |
88
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279 <genome> |
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280 #for $anno in $track.data_format.pafuseuri.annotation: |
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281 ${anno} ~ ${anno.name}, |
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282 #end for |
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283 </genome> |
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284 <useuri> |
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285 false |
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286 </useuri> |
88
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287 #else: |
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288 <genome> |
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289 #for $refgenome in $track.data_format.pafuseuri.refuri: |
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290 ${refgenome.annotation} ~ ${refgenome.annoname}, |
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291 #end for |
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292 </genome> |
93
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293 <useuri> |
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294 true |
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295 </useuri> |
88
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296 #end if |
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297 </paf> |
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298 #else if str($track.data_format.data_format_select) == "hic": |
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299 <hic> |
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300 </hic> |
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301 #else if str($track.data_format.data_format_select) == "cool": |
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302 <cool> |
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303 </cool> |
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304 #else if str($track.data_format.data_format_select) == "bed": |
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305 <bed> |
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306 <usebedscore>${track.data_format.jbstyle.usebedscore}</usebedscore> |
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307 </bed> |
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308 #else if str($track.data_format.data_format_select) == "sparql": |
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309 <label>${track.data_format.label}</label> |
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310 <sparql> |
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311 <url>${track.data_format.url}</url> |
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312 <query>${track.data_format.query}</query> |
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313 <query_refnames>${track.data_format.query_refnames}</query_refnames> |
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314 </sparql> |
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315 #end if |
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316 </options> |
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317 </track> |
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318 #end if |
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319 #end for |
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320 #end for |
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321 </tracks> |
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322 </assembly> |
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323 #end for |
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324 #end if |
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325 </root> |
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326 ]]></configfile> |
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327 </configfiles> |
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328 <inputs> |
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329 <repeat name="assemblies" min="1" title="Genome for a set of tracks" help="Tracks will display on this genome coordinates so must all match. Multiple genomes with their own sets of tracks can be added"> |
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330 <conditional name="reference_genome"> |
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331 <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"> |
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332 <option selected="True" value="indexed">Use a Galaxy server built-in genome</option> |
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333 <option value="history">Use a genome fasta file from the current history</option> |
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334 <option value="uri">Provide a URI (e.g. "https://..." for a genome reference as |
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335 tabix bgzip with predictable index file URI</option> |
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336 </param> |
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337 <when value="indexed"> |
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338 <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"> |
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339 <options from_data_table="all_fasta"> |
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340 <filter column="2" type="sort_by"/> |
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341 <validator message="No genomes are available for the selected input dataset" type="no_options"/> |
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342 </options> |
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343 </param> |
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344 </when> |
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345 <when value="history"> |
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346 <param name="genome" type="data" format="fasta" optional="true" label="Select the reference genome"/> |
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347 </when> |
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348 <when value="uri"> |
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349 <param name="uri" type="text" label="URI pointing to tabix compressed fasta - must always be on-line" |
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350 help="Warning: Requires an internet connection to view. If this URI is not available for any reason, the track will show an error. Saves disk storage"> |
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351 </param> |
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352 <param name="refname" type="text" label="Reference dbkey for tracks with this genome, such as hg38 or SacCer4"/> |
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353 </when> |
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354 </conditional> |
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355 <repeat name="track_groups" title="Track Group"> |
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356 <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."/> |
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357 <repeat name="data_tracks" title="Annotation Track"> |
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358 <conditional name="data_format" label="Track Data Selection Options"> |
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359 <param name="data_format_select" type="select" label="Track Type"> |
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360 <option value="bam">BAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option> |
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361 <option value="bed">BED track</option> |
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362 <option value="bigwig">BigWig track</option> |
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363 <option value="blastxml">Blast XML track (as GFF3)</option> |
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364 <option value="cram">CRAM track. Recommend converting to BED/bigWig unless mapping annotation needed</option> |
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365 <option value="gff">GFF/GFF3 track</option> |
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366 <option value="cool">HiC as cool/mcool/scool format files</option> |
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367 <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> |
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368 <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> |
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369 <option value="paf">PAF - Pairwise approximate mapping positions between two set of sequences</option> |
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370 <option value="vcf">VCF SNP track</option> |
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371 </param> |
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372 <when value="blastxml"> |
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373 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml"/> |
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374 <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."/> |
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375 <param name="min_gap" type="integer" min="2" value="10" label="Minimum Gap Size" help="before a new match_part feature is created"/> |
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376 <param name="is_protein" type="boolean" truevalue="true" falsevalue="false" label="Is this a protein blast search?"/> |
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377 <expand macro="track_styling_vgp"/> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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378 <expand macro="track_visibility"/> |
93
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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379 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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380 <when value="vcf"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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381 <expand macro="input_conditional" label="SNP Track Data" format="vcf,vcf_bgzip"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
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changeset
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382 <expand macro="track_styling_vcf"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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changeset
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383 <expand macro="track_visibility"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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parents:
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384 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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385 <when value="gff"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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changeset
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386 <expand macro="input_conditional" label="GFF/GFF3 Track Data" format="gff,gff3"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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387 <conditional name="match_part" label="match/match_part data"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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388 <param name="match_part_select" type="select" label="This is match/match_part data" help="Match part data selection "> |
93
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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389 <option selected="True" value="false">Not match/match part data</option> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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390 <option value="true">Match/match part data</option> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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391 </param> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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392 <when value="true"> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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393 <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)."/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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394 </when> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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395 <when value="false"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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396 </conditional> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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changeset
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397 <expand macro="track_styling_vgp"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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changeset
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398 <expand macro="track_visibility"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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399 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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400 <when value="bam"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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401 <expand macro="input_conditional" label="BAM Track Data" format="bam"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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402 <expand macro="track_visibility"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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403 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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404 <when value="bed"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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405 <expand macro="input_conditional" label="BED Track Data" format="bed"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
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changeset
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406 <expand macro="track_styling_vgp"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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changeset
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407 <expand macro="track_visibility"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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408 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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409 <when value="cram"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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410 <expand macro="input_conditional" label="CRAM Track Data" format="cram"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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411 <expand macro="track_visibility"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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412 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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413 <when value="maf"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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414 <expand macro="input_conditional" label="MAF Track Data" format="maf"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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changeset
|
415 <expand macro="track_styling_vgp"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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changeset
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416 <expand macro="track_visibility"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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417 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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418 <when value="bigwig"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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419 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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420 <expand macro="track_visibility"/> |
99
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
fubar
parents:
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421 <expand macro="track_styling_bigwig"/> |
93
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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422 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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423 <when value="paf"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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424 <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"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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425 <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"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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426 <expand macro="track_visibility"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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427 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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428 <when value="hic"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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429 <expand macro="input_conditional" label="Binary Juicebox HiC data" format="hic,juicebox_hic"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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430 <expand macro="track_visibility"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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431 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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432 <when value="cool"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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433 <expand macro="input_conditional" label="HiC data in cool/mcool/scool format" format="cool,mcool,scool"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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434 <expand macro="track_visibility"/> |
93
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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435 </when> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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436 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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437 </repeat> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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438 </repeat> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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439 </repeat> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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440 <expand macro="general_options"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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441 </inputs> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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442 <outputs> |
89
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 03400b3f71140ce62dba0db266a1f7b94b6c1a11
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443 <data format="html" name="output" label="JBrowse2: ${jbgen.session_name}"> |
31
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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444 <change_format> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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445 <when input="zipOut" value="true" format="zip"/> |
31
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
446 </change_format> |
cb4b32ca9968
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 48bc917d34af182e9158915862c8a35723660919-dirty
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|
447 </data> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
448 </outputs> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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449 <tests> |
93
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450 <test> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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451 <repeat name="assemblies"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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452 <conditional name="reference_genome"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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|
453 <param name="genome_type_select" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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454 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Merlin"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
455 <param name="genome.ext" value="fasta"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
456 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
457 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
458 <param name="category" value="Assembly properties"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
459 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
460 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
461 <param name="data_format_select" value="gff"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
462 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
463 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
464 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.gff3"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
465 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
466 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
467 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
468 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
469 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
470 <param name="data_format_select" value="bigwig"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
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471 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
472 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
473 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.bw"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
474 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
475 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
476 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
477 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
478 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
479 <param name="data_format_select" value="bed"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
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480 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
481 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
482 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/test-6.bed"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
483 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
484 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
485 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
486 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
487 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
488 <param name="data_format_select" value="vcf"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
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489 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
490 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
491 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.vcf"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
492 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
493 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
494 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
495 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
496 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
497 <param name="data_format_select" value="cram"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
498 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
499 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
500 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.cram"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
501 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
502 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
503 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
504 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
505 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
506 <param name="data_format_select" value="bam"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
507 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
508 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
509 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin-sample.bam"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
510 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
511 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
512 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
513 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
514 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
515 <param name="data_format_select" value="maf"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
516 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
517 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
518 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlinlastz.maf"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
519 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
520 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
521 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
522 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
523 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
524 <param name="data_format_select" value="blastxml"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
525 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
526 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
527 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/merlin.blastxml"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
528 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
529 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
530 </repeat> |
88
efd1d41f11b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents:
87
diff
changeset
|
531 <repeat name="data_tracks"> |
efd1d41f11b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents:
87
diff
changeset
|
532 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
533 <param name="data_format_select" value="bam"/> |
88
efd1d41f11b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents:
87
diff
changeset
|
534 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
535 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
536 <param name="annotation" value=""/> |
88
efd1d41f11b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents:
87
diff
changeset
|
537 </conditional> |
efd1d41f11b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents:
87
diff
changeset
|
538 </conditional> |
efd1d41f11b4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 22dfa93b72dddfc9eeb79ba02a7c76bc2967a5b9
fubar
parents:
87
diff
changeset
|
539 </repeat> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
540 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
541 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
542 <repeat name="assemblies"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
543 <conditional name="reference_genome"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
544 <param name="genome_type_select" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
545 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3.fa"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
546 <param name="genome.ext" value="fasta"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
547 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
548 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
549 <param name="category" value="Assembly properties"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
550 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
551 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
552 <param name="data_format_select" value="cool"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
553 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
554 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
555 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/dm3test.cool"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
556 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
557 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
558 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
559 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
560 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
561 <repeat name="assemblies"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
562 <conditional name="reference_genome"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
563 <param name="genome_type_select" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
564 <param name="genome" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Ppersica1.fa"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
565 <param name="genome.ext" value="fasta"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
566 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
567 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
568 <param name="category" value="Assembly properties"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
569 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
570 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
571 <param name="data_format_select" value="paf"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
572 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
573 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
574 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/peach-grape-map.paf"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
575 </conditional> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
576 <conditional name="pafuseuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
577 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
578 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
579 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
580 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
581 </repeat> |
91
6246925692cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents:
90
diff
changeset
|
582 <repeat name="data_tracks"> |
6246925692cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents:
90
diff
changeset
|
583 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
584 <param name="data_format_select" value="paf"/> |
91
6246925692cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents:
90
diff
changeset
|
585 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
586 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
587 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
588 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
589 <conditional name="pafuseuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
590 <param name="insource" value="uri"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
591 <repeat name="refuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
592 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa.gz"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
593 <param name="annoname" value="arabidopsis.URI"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
594 </repeat> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
595 <repeat name="refuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
596 <param name="annotation" value="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa.gz"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
597 <param name="annoname" value="Vvinifera1.URI"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
598 </repeat> |
91
6246925692cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents:
90
diff
changeset
|
599 </conditional> |
6246925692cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents:
90
diff
changeset
|
600 </conditional> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
601 </repeat> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
602 <repeat name="data_tracks"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
603 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
604 <param name="data_format_select" value="paf"/> |
91
6246925692cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents:
90
diff
changeset
|
605 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
606 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
607 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabgrapepeach.paf"/> |
91
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
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|
608 </conditional> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
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609 <conditional name="pafuseuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
610 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
611 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/arabidopsis.fa"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
612 <param name="annotation" location="https://usegalaxy.eu/static/share/ebp/jbrowse2/test-data/Vvinifera1.fa"/> |
91
6246925692cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents:
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diff
changeset
|
613 </conditional> |
6246925692cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents:
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changeset
|
614 </conditional> |
6246925692cb
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 0ff79bc5c2f228a5d56c84aac1b436d1cc62403d
fubar
parents:
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diff
changeset
|
615 </repeat> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
616 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
617 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
618 <repeat name="assemblies"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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changeset
|
619 <conditional name="reference_genome"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
620 <param name="genome_type_select" value="uri"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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diff
changeset
|
621 <param name="uri" value="https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/fasta/GRCh38.fa.gz"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
622 <param name="refname" value="hg38"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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diff
changeset
|
623 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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diff
changeset
|
624 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
625 <param name="category" value="Assembly properties"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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changeset
|
626 <repeat name="data_tracks"> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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changeset
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627 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
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changeset
|
628 <param name="data_format_select" value="hic"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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changeset
|
629 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
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changeset
|
630 <param name="insource" value="uri"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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|
631 <param name="annouri" value="https://s3.amazonaws.com/igv.broadinstitute.org/data/hic/intra_nofrag_30.hic"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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|
632 <param name="annoname" value="humanhic"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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changeset
|
633 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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|
634 </conditional> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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diff
changeset
|
635 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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changeset
|
636 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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changeset
|
637 </repeat> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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changeset
|
638 <section name="jbgen"> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
639 <param name="zipOut" value="true"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
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changeset
|
640 <param name="session_name" value="New test session"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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641 </section> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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|
642 <!-- use the following line to generate a ZIP file to inspect it --> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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643 <!--output name="output" file="jbrowse2_result02.zip" ftype="zip" compare="sim_size"--> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
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diff
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|
644 <output name="output" ftype="zip"> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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645 <assert_contents> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
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|
646 <has_archive_member path=".*" n="637" delta="10"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
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647 <has_archive_member path="index.html"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
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|
648 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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parents:
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diff
changeset
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649 <has_archive_member path="manifest.json"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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diff
changeset
|
650 <has_text text="favicon.ico"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
651 <has_text text="background_color"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
652 </has_archive_member> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
653 <has_archive_member path="galaxy.xml"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
93
diff
changeset
|
654 <is_valid_xml/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
655 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
656 <element_text_is path="./metadata/general/session_name" text="New test session"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
85
diff
changeset
|
657 </has_archive_member> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
658 <has_archive_member path="merlin.gff3_0.gz"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
659 <has_archive_member path="merlin.gff3_0.gz.tbi"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
660 <has_archive_member path="merlin.bw_1"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
661 <has_archive_member path="test-6.bed_2.gz"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
662 <has_archive_member path="merlin.vcf_3"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
663 <has_archive_member path="merlin.vcf_3.tbi"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
664 <has_archive_member path="merlin.cram_4"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
665 <has_archive_member path="merlin.cram_4.crai"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
666 <has_archive_member path="merlin-sample.bam_5"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
667 <has_archive_member path="merlin-sample.bam_5.bai"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
668 <has_archive_member path="merlinlastz.maf_6.sorted.bed.gz.tbi"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
669 <has_archive_member path="merlin.blastxml_7.gz"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
670 <has_archive_member path="dm3test.cool_9.hic"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
671 <has_archive_member path="peach-grape-map.paf_10"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
672 <has_archive_member path="arabgrapepeach.paf_11"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
673 <has_archive_member path="Merlin.fa.gz.fai"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
674 <has_archive_member path="dm3.fa.fa.gz.fai"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
675 <has_archive_member path="Ppersica1.fa.fa.gz"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
676 <has_archive_member path="Ppersica1.fa.fa.gz.fai"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
677 <has_archive_member path="Ppersica1.fa.fa.gz.gzi"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
678 <has_archive_member path="Vvinifera1.fa.fa.gz.fai"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
679 <has_archive_member path="Vvinifera1.fa.fa.gz"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
680 <has_archive_member path="Vvinifera1.fa.fa.gz.gzi"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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diff
changeset
|
681 <has_archive_member path="config.json"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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|
682 <has_json_property_with_text property="name" text="Merlin"/> |
86
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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683 </has_archive_member> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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changeset
|
684 </assert_contents> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
parents:
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changeset
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685 </output> |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
fubar
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|
686 </test> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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changeset
|
687 <test> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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changeset
|
688 <param name="autoCollection"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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689 <collection type="list" name="merlintest"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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changeset
|
690 <element name="merlin.fa" value="merlin.fa"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
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changeset
|
691 <element name="merlin.bw" value="bw/merlin.bw"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
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changeset
|
692 <element name="test-6.bed" value="bed/test-6.bed"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
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changeset
|
693 </collection> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
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changeset
|
694 </param> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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changeset
|
695 <section name="jbgen"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
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changeset
|
696 <param name="zipOut" value="true"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
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changeset
|
697 <param name="session_name" value="Collection test"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
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changeset
|
698 <param name="ucol|formcoll" value="collect"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
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|
699 </section> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
93
diff
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|
700 <!-- use the following line to generate a ZIP file to inspect it --> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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701 <!--output name="output" file="jbrowse2_result01.zip" ftype="zip" compare="sim_size"--> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
702 <output name="output" ftype="zip"> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
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|
703 <assert_contents> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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parents:
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changeset
|
704 <has_archive_member path=".*" n="611" delta="10"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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changeset
|
705 <has_archive_member path="index.html"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
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|
706 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
707 <has_archive_member path="manifest.json"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
708 <has_text text="favicon.ico"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
709 <has_text text="background_color"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
710 </has_archive_member> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
711 <has_archive_member path="galaxy.xml"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
712 <is_valid_xml/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
713 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
714 <element_text_is path="./metadata/general/session_name" text="Collection test"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
715 </has_archive_member> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
716 <has_archive_member path="jb2_webserver.py"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
717 <has_archive_member path="merlin.fa.fa.gz.gzi"/> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
718 <has_archive_member path="merlin.fa.fa.gz"/> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
719 <has_archive_member path="merlin.fa.fa.gz.fai"/> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
720 <has_archive_member path="merlin.bw"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
721 <has_archive_member path="index.html"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
722 <has_archive_member path="test-6.bed.gz"/> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
723 <has_archive_member path="test-6.bed.gz.tbi"/> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
724 </assert_contents> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
725 </output> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
726 </test> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
727 <test> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
728 <repeat name="assemblies"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
729 <conditional name="reference_genome"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
730 <param name="genome_type_select" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
731 <param name="genome" value="merlin.fa"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
732 <param name="genome.ext" value="fasta"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
733 <param name="genome.name" value="Merlin"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
734 </conditional> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
735 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
736 <param name="category" value="Default"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
737 <repeat name="data_tracks"> |
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
738 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
739 <param name="data_format_select" value="bigwig"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
740 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
741 <param name="annotation" value="bw/merlin.bw"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
742 <param name="insource" value="history"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
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diff
changeset
|
743 </conditional> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
744 </conditional> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
745 </repeat> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
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diff
changeset
|
746 </repeat> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
747 </repeat> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
748 <section name="jbgen"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
749 <param name="zipOut" value="true"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
750 </section> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
751 <output name="output"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
752 <assert_contents> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
753 <has_archive_member path="galaxy.xml"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
754 <has_text text="genome path="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
755 <has_text text="label="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
756 <has_text text="format="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
757 <has_text text="metadata"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
758 <has_text text="useuri="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
759 <has_text text="trackFile path="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
760 <has_text text="ext="bigwig""/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
761 <has_text text="format="bigwig""/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
762 </has_archive_member> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
763 </assert_contents> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
764 </output> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
765 </test> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
766 <test> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
767 <repeat name="assemblies"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
768 <conditional name="reference_genome"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
769 <param name="genome_type_select" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
770 <param name="genome" value="merlin.fa"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
771 <param name="genome.ext" value="fasta"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
772 <param name="genome.name" value="Merlin"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
773 </conditional> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
774 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
775 <param name="category" value="Default"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
776 <repeat name="data_tracks"> |
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
777 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
778 <param name="data_format_select" value="vcf"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
779 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
780 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
781 <param name="annotation" value="vcf/merlin.vcf"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
782 </conditional> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
783 </conditional> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
784 </repeat> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
785 </repeat> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
786 </repeat> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
787 <section name="jbgen"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
788 <param name="zipOut" value="true"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
789 </section> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
790 <output name="output"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
791 <assert_contents> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
792 <has_archive_member path="galaxy.xml"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
793 <has_text text="genome path="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
794 <has_text text="label="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
795 <has_text text="format="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
796 <has_text text="metadata"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
797 <has_text text="useuri="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
798 <has_text text="trackFile path="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
799 <has_text text="ext="vcf" label="merlin.vcf""/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
800 </has_archive_member> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
801 </assert_contents> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
802 </output> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
803 </test> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
804 <test> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
805 <repeat name="assemblies"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
806 <conditional name="reference_genome"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
807 <param name="genome_type_select" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
808 <param name="genome" value="merlin.fa"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
809 <param name="genome.ext" value="fasta"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
810 <param name="genome.name" value="Merlin"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
811 </conditional> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
812 </repeat> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
813 <section name="jbgen"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
814 <param name="zipOut" value="true"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
815 </section> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
816 <output name="output"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
817 <assert_contents> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
818 <has_archive_member path="galaxy.xml"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
819 <has_text text="genome path="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
820 <has_text text="label="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
821 <has_text text="useuri="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
822 <has_text text="metadata"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
823 </has_archive_member> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
824 </assert_contents> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
825 </output> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
826 </test> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
827 <test> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
828 <repeat name="assemblies"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
829 <conditional name="reference_genome"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
830 <param name="genome_type_select" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
831 <param name="genome" value="merlin.fa"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
832 <param name="genome.ext" value="fasta"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
833 <param name="genome.name" value="Merlin"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
834 </conditional> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
835 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
836 <param name="category" value="Default"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
837 <repeat name="data_tracks"> |
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
838 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
839 <param name="data_format_select" value="vcf"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
840 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
841 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
842 <param name="annotation" value="vcf/merlin.vcf"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
843 </conditional> |
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
844 </conditional> |
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
845 </repeat> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
846 </repeat> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
847 </repeat> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
848 <section name="jbgen"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
849 <param name="zipOut" value="true"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
850 </section> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
851 <output name="output"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
852 <assert_contents> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
853 <has_archive_member path="galaxy.xml"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
854 <has_text text="genome path="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
855 <has_text text="label="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
856 <has_text text="format="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
857 <has_text text="metadata"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
858 <has_text text="useuri="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
859 <has_text text="trackFile path="/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
860 <has_text text="ext="vcf" label="merlin.vcf""/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
bgruening
parents:
97
diff
changeset
|
861 </has_archive_member> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
862 </assert_contents> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
863 </output> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
864 </test> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
865 <test> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
866 <repeat name="assemblies"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
867 <conditional name="reference_genome"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
868 <param name="genome_type_select" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
869 <param name="genome" value="merlin.fa"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
870 <param name="genome.ext" value="fasta"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
871 <param name="genome.name" value="Merlin"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
872 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
873 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
874 <param name="category" value="Default"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
875 <repeat name="data_tracks"> |
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
876 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
877 <param name="data_format_select" value="gff"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
878 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
879 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
880 <param name="annotation" value="gff3/A.gff"/> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
881 </conditional> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
882 </conditional> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
883 <conditional name="match_part"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
884 <param name="match_part_select" value="false"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
885 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
886 <section name="jbcolor_scale"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
887 <conditional name="color_score"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
888 <param name="color_score_select" value="none"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
889 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
890 <conditional name="color"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
891 <param name="color_select" value="automatic"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
892 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
893 </section> |
62
ab0d6782a95f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 2b6d4a24585beb1ba5055e5d34aacb3b299b1943-dirty
fubar
parents:
60
diff
changeset
|
894 </repeat> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
895 </repeat> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
896 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
897 <param name="category" value="Ignore Scale"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
898 <repeat name="data_tracks"> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
899 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
900 <param name="data_format_select" value="gff"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
901 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
902 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
903 <param name="annotation" value="gff3/1.gff"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
904 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
905 <conditional name="match_part"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
906 <param name="match_part_select" value="false"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
907 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
908 <section name="jbcolor_scale"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
909 <conditional name="color_score"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
910 <param name="color_score_select" value="none"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
911 <conditional name="color"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
912 <param name="color_select" value="manual"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
913 <param name="style_color" value="#ff00ff"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
914 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
915 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
916 </section> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
917 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
918 </repeat> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
919 </repeat> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
920 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
921 <param name="category" value="Scaled Colour"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
922 <repeat name="data_tracks"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
923 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
924 <param name="data_format_select" value="gff"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
925 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
926 <param name="insource" value="history"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
927 <param name="annotation" value="gff3/C.gff"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
928 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
929 <conditional name="match_part"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
930 <param name="match_part_select" value="false"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
931 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
932 <section name="jbcolor_scale"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
933 <conditional name="color_score"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
934 <param name="color_score_select" value="score"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
935 <param name="score_scaling" value="linear"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
936 <conditional name="score_scales"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
937 <param name="scale_select" value="automatic"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
938 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
939 <conditional name="color_scheme"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
940 <param name="score_scheme" value="opacity"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
941 <conditional name="color"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
942 <param name="color_select" value="automatic"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
943 </conditional> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
944 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
945 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
946 </section> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
947 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
948 </repeat> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
949 <repeat name="data_tracks"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
950 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
951 <param name="data_format_select" value="gff"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
952 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
953 <param name="annotation" value="gff3/B.gff"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
954 <param name="insource" value="history"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
955 </conditional> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
956 <conditional name="match_part"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
957 <param name="match_part_select" value="false"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
958 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
959 <section name="jbcolor_scale"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
960 <conditional name="color_score"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
961 <param name="color_score_select" value="score"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
962 <param name="score_scaling" value="linear"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
963 <conditional name="score_scales"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
964 <param name="scale_select" value="automatic"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
965 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
966 <conditional name="color_scheme"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
967 <param name="score_scheme" value="opacity"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
968 <conditional name="color"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
969 <param name="color_select" value="manual"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
970 <param name="style_color" value="#0000ff"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
971 </conditional> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
972 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
973 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
974 </section> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
975 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
976 </repeat> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
977 <repeat name="data_tracks"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
978 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
979 <param name="data_format_select" value="gff"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
980 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
981 <param name="annotation" value="gff3/A.gff"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
982 <param name="insource" value="history"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
983 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
984 <conditional name="match_part"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
985 <param name="match_part_select" value="false"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
986 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
987 <section name="jbcolor_scale"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
988 <conditional name="color_score"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
989 <param name="color_score_select" value="score"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
990 <param name="score_scaling" value="linear"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
991 <conditional name="score_scales"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
992 <param name="scale_select" value="manual"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
993 <param name="minimum" value="0"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
994 <param name="maximum" value="1000"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
995 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
996 <conditional name="color_scheme"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
997 <param name="score_scheme" value="opacity"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
998 <conditional name="color"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
999 <param name="color_select" value="automatic"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
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parents:
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diff
changeset
|
1000 </conditional> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1001 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1002 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1003 </section> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1004 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1005 </repeat> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1006 <repeat name="data_tracks"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1007 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1008 <param name="data_format_select" value="gff"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1009 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1010 <param name="annotation" value="gff3/1.gff"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1011 <param name="insource" value="history"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1012 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1013 <conditional name="match_part"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1014 <param name="match_part_select" value="false"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1015 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1016 <section name="jbcolor_scale"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1017 <conditional name="color_score"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1018 <param name="color_score_select" value="score"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1019 <param name="score_scaling" value="linear"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1020 <conditional name="score_scales"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1021 <param name="scale_select" value="manual"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1022 <param name="minimum" value="0"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1023 <param name="maximum" value="1000"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1024 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1025 <conditional name="color_scheme"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1026 <param name="score_scheme" value="opacity"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1027 <conditional name="color"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1028 <param name="color_select" value="manual"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1029 <param name="style_color" value="#ff0000"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1030 </conditional> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1031 </conditional> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1032 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1033 </section> |
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
fubar
parents:
45
diff
changeset
|
1034 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1035 </repeat> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1036 </repeat> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1037 <repeat name="track_groups"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1038 <param name="category" value="Realistic"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1039 <repeat name="data_tracks"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1040 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1041 <param name="data_format_select" value="gff"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1042 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1043 <param name="annotation" value="gff3/interpro.gff"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1044 <param name="insource" value="history"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1045 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1046 <conditional name="match_part"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1047 <param name="match_part_select" value="false"/> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1048 </conditional> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1049 <section name="jbcolor_scale"> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1050 <conditional name="color_score"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1051 <param name="color_score_select" value="none"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1052 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1053 <conditional name="color"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1054 <param name="color_select" value="automatic"/> |
63
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1055 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1056 </section> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1057 </conditional> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1058 </repeat> |
ac00dcfb5d1d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f450a9a7bec7ae695a85a061bf59956b73196976
fubar
parents:
62
diff
changeset
|
1059 <repeat name="data_tracks"> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1060 <conditional name="data_format"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1061 <param name="data_format_select" value="gff"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1062 <conditional name="useuri"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1063 <param name="annotation" value="gff3/2.gff"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1064 <param name="insource" value="history"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1065 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1066 <conditional name="match_part"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1067 <param name="match_part_select" value="true"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1068 <param name="name" value="cDNA_match"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1069 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1070 <section name="jbcolor_scale"> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1071 <conditional name="color_score"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1072 <param name="color_score_select" value="none"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1073 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1074 <conditional name="color"> |
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
fubar
parents:
93
diff
changeset
|
1075 <param name="color_select" value="automatic"/> |
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1076 </conditional> |
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
fubar
parents:
92
diff
changeset
|
1077 </section> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
fubar
parents:
diff
changeset
|
1078 </conditional> |
63
ac00dcfb5d1d
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diff
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1079 </repeat> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1080 </repeat> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1081 </repeat> |
98
b1260bca5fdc
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|
1082 <section name="jbgen"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1083 <param name="zipOut" value="true"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1084 </section> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
diff
changeset
|
1085 <output name="output"> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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diff
changeset
|
1086 <assert_contents> |
98
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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diff
changeset
|
1087 <has_archive_member path="A.gff"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1088 <has_archive_member path="B.gff"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1089 <has_archive_member path="C.gff"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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changeset
|
1090 <has_archive_member path="interpro.gff"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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diff
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|
1091 <has_archive_member path="1.gff"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1092 <has_archive_member path="2.gff"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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diff
changeset
|
1093 <has_archive_member path="galaxy.xml"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1094 <is_valid_xml/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1095 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1096 <element_text_is path="./metadata/general/session_name" text="New JBrowse2 session"/> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1097 </has_archive_member> |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1098 </assert_contents> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1099 </output> |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1100 </test> |
98
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1101 <test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1102 <repeat name="assemblies"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1103 <conditional name="reference_genome"> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1104 <param name="genome_type_select" value="history"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1105 <param name="genome" value="merlin.fa"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1106 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1107 <repeat name="track_groups"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1108 <param name="category" value="Auto Coloured"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1109 <repeat name="data_tracks"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1110 <conditional name="data_format"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1111 <param name="data_format_select" value="cram"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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|
1112 <param name="annotation" value="cram/merlin-sample.cram"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1113 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1114 </repeat> |
b1260bca5fdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1115 </repeat> |
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1116 </repeat> |
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1117 <section name="jbgen"> |
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1118 <param name="zipOut" value="true"/> |
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1119 </section> |
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1120 <output name="output" ftype="zip"> |
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1121 <assert_contents> |
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1122 <!-- roughly 590 files in an archive --> |
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1123 <has_archive_member path=".*" n="608" delta="30"/> |
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1124 <has_archive_member path="index.html"/> |
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1125 <has_archive_member path="static/media/roboto-latin-400-normal.3f2b9a42f643e62a49b7.woff"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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1126 <has_archive_member path="manifest.json"> |
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1127 <has_text text="favicon.ico"/> |
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1128 <has_text text="background_color"/> |
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1129 </has_archive_member> |
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1130 <has_archive_member path="merlin.fa.fa.gz.fai"/> |
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1131 <has_archive_member path="galaxy.xml"> |
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1132 <is_valid_xml/> |
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1133 <has_n_elements_with_path path="./metadata/general/session_name" n="1"/> |
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1134 <element_text_is path="./metadata/general/session_name" text="New JBrowse2 session"/> |
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1135 </has_archive_member> |
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1136 </assert_contents> |
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1137 </output> |
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1138 </test> |
0
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1139 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1140 <help><![CDATA[ |
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1141 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1142 JBrowse2-in-Galaxy |
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1143 ================== |
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1144 |
98
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1145 JBrowse2-in-Galaxy offers a highly configurable, workflow-compatible Genome viewer. |
0
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1146 |
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1147 |
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|
1148 Use and local viewing |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1149 ===================== |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1150 |
107
a074cd6b5905
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|
1151 Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks. |
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1152 |
112
56f9a6e0fe80
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1153 Many Galaxy datatypes can be turned into a track for display - in all cases, the selected reference genome must have been |
99
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1154 used to generate the data: |
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1155 |
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1156 bam |
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1157 bed |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1158 bigwig |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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|
1159 blastxml |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1160 cram |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1161 gff3 |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1162 hic |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1163 maf |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1164 paf |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1165 vcf |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1166 |
107
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1167 Note that cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. Otherwise conversion to bed is recommended to slim them down. |
99
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1168 Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended. |
7
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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1169 |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1170 A JBrowse2 history item can be opened by viewing it (the "eye" icon). |
7
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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1171 |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1172 Overview |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1173 -------- |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1174 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1175 JBrowse is a fast, embeddable genome browser built completely with |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1176 JavaScript and HTML5. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1177 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1178 The JBrowse-in-Galaxy (JiG) tool was written to help build complex |
7
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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|
1179 JBrowse installations straight from Galaxy. It allows you to build up a JBrowse instance without worrying |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1180 about how to run the command line tools to format your data, and which |
7
b04fd993b31e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 53a108d8153c955044ae7eb8cb06bdcfd0036717
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1181 options need to be supplied and where. |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1182 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1183 Options |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1184 ------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1185 |
17
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1186 **Reference or Assembly** |
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1187 |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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1188 Choose either a built-in or select one from your history. |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1189 |
17
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1190 Track coordinates and contig names *must* match this reference precisely |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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1191 or they will not display. |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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1192 |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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1193 **Track Groups** represent a set of tracks in a single category. |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1194 |
99
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1195 |
0
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1196 Annotation Tracks |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1197 ----------------- |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1198 |
112
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1199 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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1200 BED |
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1201 ~~~ |
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1202 |
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1203 Bed feature annotation usually requires clicking on the feature. |
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1204 |
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1205 Bed files created by the *Bigwig extremes to bed features* tool have the score in column 5 |
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1206 set to *1* for regions above the quantile and *-1* for regions below. It is possible to set an advanced option for each bed track, to use the bed score in column 5 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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1207 for the feature colour, giving red and blue using a JBrowse2 plugin, so they are easy to distinguish in a combined track. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 566509061b742b73c8dd1a1db6813fbf6a7a3792
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1208 |
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1209 |
86
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1210 MAF |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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1211 ~~~ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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1212 |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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1213 For history references, the name of the reference genome dataset in your history is very important for MAF tracks, |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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1214 because it becomes the "dbkey" for that reference. So, it must be exactly the same as the genome name (dbkey) used |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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|
1215 when making the MAF, typically in the Lastz tool. |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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|
1216 |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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1217 If you used "hg38" as the reference in Lastz, that is exactly what the reference fasta should be named for any MAF track. |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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1218 Change it using the "pencil" icon on the reference data in your history. Any other name, such as "hg38.fasta" |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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1219 will cause the MAF track to show no data since there are no matches with that reference dbkey. |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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|
1220 |
0fae1d68347f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit f09abc1f5ef8d261dff2d1b0063fff99a1b25f93
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1221 |
0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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parents:
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changeset
|
1222 GFF3/BED |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1223 ~~~~~~~~ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1224 |
17
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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|
1225 Standard feature tracks. They usually highlight genes, mRNAs and other features of interest along a genomic region. |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1226 |
5
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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diff
changeset
|
1227 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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changeset
|
1228 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is |
efc64d8f4b72
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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changeset
|
1229 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works |
17
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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|
1230 well for relatively sparse bed files. A better option is to make a bigwig track using a set of windows based on the |
4c201a3d4755
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a37bfdfc108501b11c7b2aa15efb1bd16f0c4b66
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|
1231 lengths of each assembly or reference contig. |
5
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
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|
1232 |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1233 BAM Pileups |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1234 ~~~~~~~~~~~ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1235 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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changeset
|
1236 We support BAM files and can automatically generate SNP tracks based on |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1237 that bam data. |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1238 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1239 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1240 BlastXML |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1241 ~~~~~~~~ |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1242 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1243 JiG now supports both blastn and blastp datasets. JiG internally uses a |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1244 blastXML to gapped GFF3 tool to convert your blastxml datasets into a |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1245 format amenable to visualization in JBrowse. This tool is also |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1246 available separately from the IUC on the toolshed. |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1247 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1248 **Minimum Gap Size** reflects how long a gap must be before it becomes a |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1249 real gap in the processed gff3 file. In the picture above, various sizes |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1250 of gaps can be seen. If the minimum gap size was set much higher, say |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1251 100nt, many of the smaller gaps would disappear, and the features on |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1252 both sides would be merged into one, longer feature. This setting is |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1253 inversely proportional to runtime and output file size. *Do not set this |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1254 to a low value for large datasets*. By setting this number lower, you |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1255 will have extremely large outputs and extremely long runtimes. The |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1256 default was configured based off of the author's experience, but the |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1257 author only works on small viruses. It is *strongly* recommended that |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1258 you filter your blast results before display, e.g. picking out the top |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1259 10 hits or so. |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1260 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1261 **Protein blast search** option merely informs underlying tools that |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1262 they should adjust feature locations by 3x. |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1263 |
99
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1264 Local viewing |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1265 ============= |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1266 |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1267 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. |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1268 This can be shared and viewed without Galaxy. |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1269 |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1270 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, |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1271 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 |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1272 directory to the first level in that zip archive. It contains a file named *jb2_webserver.py* |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1273 |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1274 With python3 installed, |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1275 |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1276 *python3 jb2_webserver.py* |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1277 |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1278 will serve the unarchived JBrowse2 configuration from the same directory as the python script automatically. If a new browser window does not open, |
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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1279 but the script appears to be running, try pointing your web browser to the default of *localhost:8080* |
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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1280 |
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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|
1281 ]]></help> |
97
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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1282 <expand macro="citations"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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1283 <expand macro="creators"/> |
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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1284 </tool> |