Mercurial > repos > fubar > jbrowse2
annotate macros.xml @ 100:666c07b60cd2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
| author | fubar |
|---|---|
| date | Fri, 21 Jun 2024 23:49:10 +0000 |
| parents | 990291e918c7 |
| children | e4ba5f1da6ef |
| rev | line source |
|---|---|
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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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1 <macros> |
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100
666c07b60cd2
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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2 <token name="@TOOL_VERSION@">2.12.2</token> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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3 <xml name="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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4 <edam_topics> |
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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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5 <edam_topic>topic_3307</edam_topic> |
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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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6 <edam_topic>topic_0092</edam_topic> |
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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 </edam_topics> |
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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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8 <edam_operations> |
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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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9 <edam_operation>operation_0573</edam_operation> |
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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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10 <edam_operation>operation_0564</edam_operation> |
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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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11 </edam_operations> |
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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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12 </xml> |
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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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13 <xml name="requirements"> |
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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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14 <requirements> |
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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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15 <requirement type="package" version="@TOOL_VERSION@">jbrowse2</requirement> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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16 <requirement type="package" version="1.82">biopython</requirement> |
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19
bde6b1d09f7d
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1290bf486bc55c02fecd0327de10a28655a18e81-dirty
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17 <requirement type="package" version="0.7.1">bcbio-gff</requirement> |
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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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18 <requirement type="package" version="1.19">samtools</requirement> |
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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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19 <requirement type="package" version="6.0.1">pyyaml</requirement> |
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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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20 <requirement type="package" version="1.11">tabix</requirement> |
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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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21 <requirement type="package" version="4.6.0">findutils</requirement> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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22 <requirement type="package" version="0.0.12-0">hictk</requirement> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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23 <requirement type="package" version="3.0">zip</requirement> |
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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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24 <yield/> |
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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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25 </requirements> |
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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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26 </xml> |
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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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27 <token name="@DATA_DIR@">\$GALAXY_JBROWSE_SHARED_DIR</token> |
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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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28 <token name="@VERSION_SUFFIX@">0</token> |
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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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29 <xml name="creators"> |
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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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30 <creator> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 44d8fc559ecf5463a8f753561976fa26686c96f6
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31 <person givenName="Helena" familyName="Rasche" url="https://github.com/hexylena"/> |
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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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32 <person givenName="Anthony" familyName="Bretaudeau" url="https://github.com/abretaud"/> |
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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 <person givenName="Ross" familyName="Lazarus" url="https://github.com/fubar2/"/> |
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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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34 </creator> |
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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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35 </xml> |
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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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36 <xml name="genome_selector" token_help="" token_label="Fasta sequences" token_optional="False"> |
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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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37 <conditional name="reference_genome"> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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38 <param name="genome_type_select" type="select" label="Reference genome to display" help="Built-in references"> |
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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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39 <option selected="True" value="indexed">Use a built-in genome</option> |
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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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40 <option value="history">Use a genome from history</option> |
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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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41 </param> |
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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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42 <when value="indexed"> |
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43 <param name="genomes" type="select" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@"> |
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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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44 <options from_data_table="all_fasta"> |
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45 <filter column="2" type="sort_by"/> |
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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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46 <validator message="No genomes are available for the selected input dataset" type="no_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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47 </options> |
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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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48 </param> |
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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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49 </when> |
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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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50 <when value="history"> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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51 <param name="genomes" type="data" format="fasta" optional="@OPTIONAL@" label="@LABEL@" help="@HELP@" multiple="True"/> |
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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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52 </when> |
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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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53 </conditional> |
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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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54 </xml> |
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55 <xml name="auto_manual_tk" token_cond_label="Color" token_cond_name="color" token_select_label="Color Specification" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection"> |
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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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56 <conditional name="@COND_NAME@" label="@COND_LABEL@"> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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57 <param name="@SELECT_NAME@" type="select" label="@SELECT_LABEL@"> |
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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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58 <option value="automatic" selected="true">@AUTOMATIC_LABEL@</option> |
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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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59 <option value="manual">@MANUAL_LABEL@</option> |
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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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60 </param> |
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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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61 <when value="automatic"> |
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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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62 </when> |
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63 <when value="manual"> |
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64 <yield/> |
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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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65 </when> |
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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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66 </conditional> |
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67 </xml> |
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68 <xml name="jb_color" token_label="JBrowse style.color" token_name="style_color" token_value="goldenrod" token_help="Basic color of features. Most glyphs interpret this as the fill color of the rectangle they draw. Color syntax is the same as that used for CSS"> |
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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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69 <param name="@NAME@" type="color" value="@VALUE@" label="@LABEL@" help="@HELP@"> |
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70 <sanitizer> |
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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 <valid initial="string.letters,string.digits"> |
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72 <add value="#"/> |
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73 </valid> |
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74 </sanitizer> |
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75 </param> |
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76 </xml> |
|
97
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77 <xml name="auto_color" token_cond_label="Color" token_cond_name="color" token_select_label="Color Selection" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection"> |
|
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78 <expand macro="auto_manual_tk" cond_label="@COND_LABEL@" cond_name="@COND_NAME@" select_label="@SELECT_LABEL@" select_name="@SELECT_NAME@" automatic_label="@AUTOMATIC_LABEL@" manual_label="@MANUAL_LABEL@"> |
|
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79 <expand macro="jb_color"/> |
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80 <yield/> |
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81 </expand> |
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82 </xml> |
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83 <xml name="brewer_scheme"> |
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97
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84 <param name="brewer_scheme" type="select" label="Brewer color Scheme"> |
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85 <option value="BrBg">BrBg: Brown - Blue Green</option> |
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86 <option value="PiYg">PiYg: Pink - Yellow Green</option> |
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87 <option value="PRGn">PRGn: Purple Red - Green</option> |
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88 <option value="PuOr">PuOr: Purple - Orange</option> |
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89 <option value="RdBu" selected="true">RdBu: Red - Blue</option> |
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90 <option value="RdGy">RdGy: Red - Gray</option> |
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91 <option value="RdYlBu">RdYlBu: Red - Yellow - Blue</option> |
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92 <option value="RdYlGn">RdYlBu: Red - Yellow - Green</option> |
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93 <option value="Spectral">Spectral</option> |
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94 </param> |
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95 </xml> |
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96 <xml name="general_options"> |
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97 <section name="jbgen" title="General JBrowse Options [Advanced]" expanded="false"> |
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46
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98 <conditional name="ucol"> |
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97
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99 <param name="formcoll" type="select" label="Convert a collection of track files rather than filling in the tool form" help="A collection of bam/vcf and other track types will be converted into a JBrowse2 automatically"> |
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46
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100 <option value="form" selected="true">Fill in the tool form to specify tracks for the output JBrowse2</option> |
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101 <option value="collect">Convert a collection of suitable track files</option> |
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102 </param> |
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103 <when value="collect"> |
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97
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104 <param name="autoCollection" type="data_collection" label="Collection of bed, bam and other track files"/> |
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46
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105 </when> |
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98
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106 <when value="form"/> |
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46
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107 </conditional> |
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98
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108 <param name="zipOut" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Create a zip archive for downloading rather than viewing" help="Default is to make an interactive browser appear when the 'eye' icon is activated"/> |
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97
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109 <param name="defaultLocation" type="text" value="" label="Subset to display to new users" help="Initial subset to be shown for users who have never visited the browser before. Example: 'ctgA:1234..5678"/> |
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98
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110 <param name="session_name" type="text" value="New JBrowse2 session" label="Session name" help="Displayed at the top of the window"/> |
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97
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111 <param name="enableAnalytics" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Enable analytics" help="Will send usage data to Google Analytics, see https://github.com/GMOD/jbrowse-components/issues/1166"/> |
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112 <param name="primary_color" type="color" value="#0D233F" label="Primary color"> |
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0
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113 <sanitizer> |
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114 <valid initial="string.ascii_letters,string.digits"> |
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97
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115 <add value="#"/> |
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116 </valid> |
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117 </sanitizer> |
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118 </param> |
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97
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119 <param name="secondary_color" type="color" value="#721E63" label="Secondary color"> |
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0
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120 <sanitizer> |
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121 <valid initial="string.ascii_letters,string.digits"> |
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97
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122 <add value="#"/> |
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0
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123 </valid> |
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124 </sanitizer> |
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125 </param> |
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97
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126 <param name="tertiary_color" type="color" value="#135560" label="Tertiary color"> |
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0
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127 <sanitizer> |
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128 <valid initial="string.ascii_letters,string.digits"> |
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97
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129 <add value="#"/> |
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130 </valid> |
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131 </sanitizer> |
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132 </param> |
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133 <param name="quaternary_color" type="color" value="#FFB11D" label="Quaternary color"> |
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134 <sanitizer> |
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135 <valid initial="string.ascii_letters,string.digits"> |
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136 <add value="#"/> |
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137 </valid> |
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138 </sanitizer> |
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139 </param> |
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97
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140 <param name="font_size" type="integer" value="10" label="Font size"/> |
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0
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141 </section> |
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142 </xml> |
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143 <xml name="color_selection_minmax"> |
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144 <section name="jbcolor" title="JBrowse Color Options [Advanced]" expanded="false"> |
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97
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145 <!-- Abuse auto/manual for bicolor pivot. Means we'll have to handle the |
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0
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146 auto case as well, but may be safe to just say "brewer colors? Pff, |
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147 red/blue" --> |
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148 <expand macro="auto_manual_tk" token_cond_label="Color" token_cond_name="color" token_select_label="Color Selection" token_select_name="color_select" token_automatic_label="Automatically selected" token_manual_label="Manual Color Selection"> |
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149 <expand macro="jb_color" label="JBrowse style.pos_color" name="style_pos_color" value="blue" help="CSS color, default 'blue'. When drawing bicolor plots, the fill color to use for values that are above the pivot point."/> |
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150 <expand macro="jb_color" label="JBrowse style.neg_color" name="style_neg_color" value="red" help=" CSS color, default 'red'. When drawing bicolor plots, the fill color to use for values that are below the pivot point."/> |
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151 </expand> |
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152 <conditional name="bicolor_pivot" label="Bicolor Pivot"> |
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153 <param name="bicolor_pivot_select" type="select" label="Bicolor Pivot"> |
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154 <option value="zero" selected="true">Zero</option> |
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155 <option value="mean">Mean</option> |
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156 <option value="custom">Custom Value</option> |
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157 </param> |
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158 <when value="zero"/> |
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159 <when value="mean"/> |
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160 <when value="custom"> |
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161 <param name="pivot_point" type="float" value="0.0" label="JBrowse style.bicolor_pivot" help="Where to change from pos_color to neg_color when drawing bicolor plots."/> |
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162 </when> |
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163 </conditional> |
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164 </section> |
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165 </xml> |
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166 <xml name="color_selection" token_scaling_lin_select="true" token_scaling_log_select="false"> |
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167 <section name="jbcolor_scale" title="JBrowse Feature Score Scaling & Coloring Options [Advanced]" expanded="false"> |
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168 <conditional name="color_score" label="JBrowse style.color & Score relationship"> |
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169 <param name="color_score_select" type="select" label="Color Score Algorithm" help="How to color the features. If it is based on score, then features with a score attribute anywhere in their hierachy will have their color affected by the score. If you choose to ignore the score, then you'll be able to select a single solid color for every feature in the track"> |
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170 <option value="score">Based on score</option> |
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171 <option value="none" selected="true">Ignore score</option> |
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172 </param> |
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173 <when value="none"> |
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174 <!-- When no scaling is done, no scores available, then just let the |
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175 user choose a base color for the track --> |
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176 <expand macro="auto_color"/> |
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177 </when> |
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178 <when value="score"> |
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179 <!-- Scaling --> |
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180 <param name="score_scaling" type="select" label="JBrowse style.color function's score scaling" help="How should the colors be distributed across the values? For blast results which distributes scores on the scale of approximately [1e-500, 10], it makes sense to request a logarithmic scaling of the color values. Logarithmic is indeed the default for blast. However other analysis methods may produce scores on ranges such as [0, 100] where a linear scale would be more appropriate for color distribution."> |
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181 <option value="linear" selected="@SCALING_LIN_SELECT@">Linear scaling</option> |
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182 <option value="logarithmic" selected="false">Logarithmic scaling</option> |
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183 <option value="blast" selected="@SCALING_LOG_SELECT@">Blast scaling</option> |
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184 </param> |
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185 <!-- Scaling Bounds --> |
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186 <conditional name="score_scales" label="Minimum/Maximum values for track scores"> |
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187 <param name="scale_select" type="select" label="How should minimum and maximum values be determined for the scores of the features"> |
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188 <option value="automatic" selected="true">Automatically determined</option> |
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189 <option value="manual">Manually specify minimum and maximum expected scores for the feature track</option> |
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190 </param> |
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191 <when value="automatic"/> |
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192 <when value="manual"> |
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193 <param name="minimum" type="integer" value="0" label="Minimum expected score"/> |
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194 <param name="maximum" type="integer" value="100" label="Maximum expected score"/> |
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195 </when> |
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196 </conditional> |
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197 <!-- Scale color --> |
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198 <conditional name="color_scheme" label="Color Scheme for scored features"> |
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199 <param name="score_scheme" type="select" label="JBrowse style.color function's color scheme for scored values"> |
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200 <option value="opacity">Opacity (high scores = 1.0 opacity)</option> |
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201 <!--<option value="brewer">Brewer Color Schemes</option>--> |
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202 </param> |
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203 <when value="opacity"> |
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204 <!-- Single color selection mode --> |
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205 <expand macro="auto_color"/> |
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206 </when> |
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207 <!--<when value="brewer">--> |
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208 <!--[> Brewer continuum selection <]--> |
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209 <!--<expand macro="brewer_scheme" />--> |
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210 <!--</when>--> |
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211 </conditional> |
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212 </when> |
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213 </conditional> |
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214 </section> |
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215 </xml> |
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216 <xml name="track_visibility"> |
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217 <param name="track_visibility" type="select" label="Track Visibility"> |
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218 <option value="default_off">Off when browser opens</option> |
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219 <option value="default_on" selected="true">On when browser opens</option> |
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220 </param> |
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221 </xml> |
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222 <xml name="track_styling_linear"> |
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223 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/> |
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224 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/> |
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225 <param name="display_mode" type="select" label="Display mode"> |
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226 <option value="normal" selected="true">normal</option> |
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227 <option value="compact">compact</option> |
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228 <option value="reducedRepresentation">reducedRepresentation</option> |
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229 <option value="collapse">collapse</option> |
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230 </param> |
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97
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231 <param name="max_height" type="integer" value="600" label="Max height" help="Maximum height that the track is permitted to reach in pixels."/> |
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232 </xml> |
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85
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233 <xml name="track_styling_vgp"> |
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234 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
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97
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235 <param name="show_labels" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show labels"/> |
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236 <param name="show_descriptions" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Show descriptions"/> |
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237 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
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238 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> |
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5
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239 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> |
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240 <option value="LinearArcDisplay">LinearArcDisplay</option> |
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241 </param> |
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242 </section> |
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243 </xml> |
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244 <xml name="track_styling_feature"> |
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245 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
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246 <conditional name="track_style"> |
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247 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
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248 <option value="LinearBasicDisplay" selected="true">LinearBasicDisplay</option> |
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249 <option value="LinearPileupDisplay">LinearPileupDisplay - good for dense tracks at scale</option> |
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250 <option value="LinearArcDisplay">LinearArcDisplay</option> |
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251 </param> |
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252 <when value="LinearPileupDisplay"> |
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253 <expand macro="track_styling_linear"/> |
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254 </when> |
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255 <when value="LinearBasicDisplay"> |
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256 <expand macro="track_styling_linear"/> |
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257 <!-- examples: https://github.com/GMOD/jbrowse-components/discussions/2729 |
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258 and https://github.com/GMOD/jbrowse-components/blob/main/plugins/svg/src/SvgFeatureRenderer/configSchema.ts#L41 --> |
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259 <param name="label" type="text" value="jexl:get(feature,'name') || get(feature,'id')" label="Features label" help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> |
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260 <sanitizer> |
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261 <valid initial="default"> |
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262 <add value="|"/> |
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263 <add value="{"/> |
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264 <add value="}"/> |
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265 <add value="!"/> |
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266 <add value="?"/> |
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267 <add value="+"/> |
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268 <add value="="/> |
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269 <add value="'"/> |
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270 </valid> |
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271 </sanitizer> |
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272 </param> |
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273 <param name="description" type="text" value="jexl:get(feature,'note') || get(feature,'description')" label="Features description" help="See https://jbrowse.org/jb2/docs/config_guide/#configuration-callbacks for syntax"> |
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274 <sanitizer> |
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275 <valid initial="default"> |
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276 <add value="|"/> |
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277 <add value="{"/> |
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278 <add value="}"/> |
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279 <add value="!"/> |
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280 <add value="?"/> |
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281 <add value="+"/> |
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282 <add value="="/> |
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283 <add value="'"/> |
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284 </valid> |
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285 </sanitizer> |
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286 </param> |
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287 </when> |
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288 <when value="LinearArcDisplay"/> |
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289 </conditional> |
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290 </section> |
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291 </xml> |
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292 <xml name="track_styling_xam"> |
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293 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
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294 <conditional name="track_style"> |
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295 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
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296 <option value="LinearAlignmentsDisplay" selected="true">LinearAlignmentsDisplay</option> |
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297 <option value="LinearPileupDisplay">LinearPileupDisplay</option> |
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298 <option value="LinearSNPCoverageDisplay">LinearSNPCoverageDisplay</option> |
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62
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299 <option value="LinearReadArcsDisplay">LinearReadArcsDisplay</option> |
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300 <option value="LinearReadCloudDisplay">LinearReadCloudDisplay</option> |
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0
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301 </param> |
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62
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302 <!-- TODO check if possible to handle more options than just the display style--> |
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303 <when value="LinearAlignmentsDisplay"/> |
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304 <when value="LinearPileupDisplay"/> |
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305 <when value="LinearSNPCoverageDisplay"> |
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97
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306 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/> |
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307 <param name="minScore" type="integer" value="" optional="true" label="Min score"/> |
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308 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/> |
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0
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309 </when> |
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62
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310 <when value="LinearReadArcsDisplay"/> |
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311 <when value="LinearReadCloudDisplay"/> |
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312 </conditional> |
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313 </section> |
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314 </xml> |
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315 <xml name="track_styling_vcf"> |
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316 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
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317 <conditional name="track_style"> |
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318 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
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319 <option value="LinearVariantDisplay" selected="true">LinearVariantDisplay</option> |
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62
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320 <option value="LinearPairedArcDisplay">LinearPairedArcDisplay</option> |
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321 </param> |
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322 <when value="LinearVariantDisplay"> |
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323 <expand macro="track_styling_linear"/> |
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324 </when> |
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62
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325 <when value="LinearPairedArcDisplay"/> |
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326 </conditional> |
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327 </section> |
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328 </xml> |
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329 <xml name="track_styling_bigwig"> |
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330 <section name="jbstyle" title="JBrowse Styling Options [Advanced]" expanded="false"> |
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331 <conditional name="track_style"> |
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332 <param name="display" type="select" label="Display style" help="How the track will be displayed by default"> |
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333 <option value="LinearWiggleDisplay" selected="true">LinearWiggleDisplay</option> |
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334 </param> |
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335 <when value="LinearWiggleDisplay"> |
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99
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336 <param name="color" type="color" value="#135560" label="Wiggle colour"> |
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337 <sanitizer> |
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338 <valid initial="string.ascii_letters,string.digits"> |
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339 <add value="#"/> |
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340 </valid> |
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341 </sanitizer> |
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342 </param> |
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0
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343 <param name="autoscale" type="select" label="Autoscale type"> |
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344 <option value="local" selected="true">Local</option> |
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345 <option value="global">Global</option> |
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346 <option value="globalsd">Global ± 3σ</option> |
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347 <option value="localsd">Local ± 3σ</option> |
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348 </param> |
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97
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349 <param name="resolution" type="integer" value="1" label="Resolution"/> |
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350 <param name="summaryScoreMode" type="select" label="Autoscale type"> |
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351 <option value="max">Max</option> |
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352 <option value="min">Min</option> |
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353 <option value="avg">Avg</option> |
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354 <option value="whiskers" selected="true">Whiskers (combines all three)</option> |
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355 </param> |
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97
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356 <param name="filled" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Fill in histogram"/> |
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357 <param name="scaleType" type="select" label="Autoscale type"> |
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358 <option value="linear" selected="true">Linear</option> |
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359 <option value="log">Log</option> |
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360 </param> |
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97
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361 <param name="displayCrossHatches" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Draw cross hatches"/> |
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362 <param name="minScore" type="integer" value="" optional="true" label="Min score"/> |
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363 <param name="maxScore" type="integer" value="" optional="true" label="Max score"/> |
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0
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364 </when> |
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365 </conditional> |
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366 </section> |
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367 </xml> |
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368 <xml name="track_menu"> |
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369 <section name="jbmenu" title="JBrowse Contextual Menu options [Advanced]" expanded="false"> |
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370 <repeat name="track_menu" title="Track Menu"> |
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97
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371 <param name="menu_action" type="select" label="Menu action" help="Action performed when user clicks on the menu"> |
|
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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372 <option value="iframeDialog" selected="true">iframeDialog: causes the given url to be opened in a popup dialog box within JBrowse, in an iframe element.</option> |
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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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373 <option value="newWindow">newWindow: causes the given url to be opened in a new browser window.</option> |
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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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374 <option value="navigateTo">navigateTo: opens the given url in the same browser window, navigating the user away from JBrowse.</option> |
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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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375 </param> |
|
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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376 <param name="menu_label" type="text" label="Menu label" help="Will be displayed in the contextual menu on each feature ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> |
|
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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377 <expand macro="menu_sanitize"/> |
|
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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378 </param> |
|
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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379 <param name="menu_title" type="text" label="Menu title" help="Will be displayed in the popup title bar if displayed ({id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> |
|
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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380 <expand macro="menu_sanitize"/> |
|
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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381 </param> |
|
97
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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382 <param name="menu_url" type="text" label="Menu url" help="Destination URL ({name}, {id}, {type}, {start}, {end}, {strand} variables will be interpreted)"> |
|
74074746ccd8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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383 <expand macro="menu_sanitize"/> |
|
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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384 </param> |
|
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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385 <param name="menu_icon" type="select" label="Menu icon" help="Icon to display next to menu label"> |
|
0
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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386 <option value="dijitIconBookmark" selected="true">Bookmark</option> |
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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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387 <option value="dijitIconSave">Save</option> |
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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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388 <option value="dijitIconPrint">Print</option> |
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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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389 <option value="dijitIconCut">Cut</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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390 <option value="dijitIconCopy">Copy</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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391 <option value="dijitIconClear">Clear</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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392 <option value="dijitIconDelete">Delete</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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393 <option value="dijitIconUndo">Undo</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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394 <option value="dijitIconEdit">Edit</option> |
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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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395 <option value="dijitIconNewTask">New Task</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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396 <option value="dijitIconEditTask">Edit Task</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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397 <option value="dijitIconEditProperty">Edit Property</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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398 <option value="dijitIconTask">Task</option> |
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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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399 <option value="dijitIconFilter">Filter</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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400 <option value="dijitIconConfigure">Configure</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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401 <option value="dijitIconSearch">Search</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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402 <option value="dijitIconApplication">Application</option> |
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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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403 <option value="dijitIconChart">Chart</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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404 <option value="dijitIconConnector">Connector</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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405 <option value="dijitIconDatabase">Database</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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406 <option value="dijitIconDocuments">Documents</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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407 <option value="dijitIconMail">Mail</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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408 <option value="dijitLeaf">Leaf</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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409 <option value="dijitIconFile">File</option> |
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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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410 <option value="dijitIconFunction">Function</option> |
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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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411 <option value="dijitIconKey">Key</option> |
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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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412 <option value="dijitIconPackage">Package</option> |
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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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413 <option value="dijitIconSample">Sample</option> |
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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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414 <option value="dijitIconTable">Table</option> |
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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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415 <option value="dijitIconUsers">Users</option> |
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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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416 <option value="dijitIconFolderClosed">Folder Closed</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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417 <option value="dijitIconFolderOpen">Folder Open</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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418 <option value="dijitIconError">Error</option> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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419 </param> |
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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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420 </repeat> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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421 </section> |
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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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422 </xml> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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423 <xml name="menu_sanitize"> |
|
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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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424 <sanitizer> |
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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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425 <valid> |
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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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426 <add value="{"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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427 <add value="}"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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428 <add value="!"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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429 <add value="?"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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430 <add value="&"/> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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431 <add value="+"/> |
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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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432 <add value="="/> |
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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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433 <add value="'"/> |
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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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434 <add value="""/> |
|
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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435 </valid> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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436 </sanitizer> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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437 </xml> |
|
d78175596286
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit cd77dffaad652cfb75b98bde5231beaa6d63cd5b-dirty
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438 <xml name="input_conditional" token_label="Track Data" token_format="data"> |
|
46
4181e97c70a7
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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diff
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439 <conditional name="useuri"> |
|
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 <param name="insource" type="select" label="Define track data as a history file or an internet URI" help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> |
|
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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441 <option value="history" selected="true">Track data from a history file</option> |
|
99
990291e918c7
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
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442 <option value="uri">Tabix data URI: Internet connection required to view. Tabix index files must be available</option> |
|
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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443 </param> |
|
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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444 <when value="history"> |
|
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 <param name="annotation" type="data" format="@FORMAT@" optional="true" label="@LABEL@" multiple="True"/> |
|
93
4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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446 </when> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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447 <when value="uri"> |
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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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448 <param name="annouri" type="text" label="@LABEL@" help="Requires internet. Will show an error if not online. Saves all the tabix file disk storage"/> |
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449 <param name="annoname" type="text" label="Short name for track display"> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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450 <sanitizer invalid_char="_"> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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451 <valid initial="string.printable"> |
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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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452 <remove value="'"/> |
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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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453 </valid> |
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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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454 </sanitizer> |
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46
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 3a43e9e0ffce0966101203102e769d1ced28618a
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455 </param> |
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456 </when> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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457 </conditional> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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458 </xml> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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459 <xml name="pafref_conditional" token_label="Track Data" token_format="data"> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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460 <conditional name="pafuseuri"> |
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461 <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" help="Multiple references can be used for mashmap PAF. A URI source requires all the associated tabix index files to be in place."> |
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462 <option value="history" selected="true">PAF reference comparison genome from a history file</option> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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463 <option value="uri">PAF reference comparison genome tabix .gz URI with index files at the corresponding URIs</option> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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464 </param> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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465 <when value="history"> |
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466 <param name="annotation" type="data" format="@FORMAT@" label="@LABEL@" help="Add all PAF reference comparison genomes used to make the PAF" multiple="true"/> |
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467 </when> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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468 <when value="uri"> |
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4c517a0041a8
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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469 <repeat name="refuri" title="PAF reference comparison genome URI" min="1"> |
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470 <param name="annotation" type="text" label="@LABEL@"/> |
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471 <param name="annoname" type="text" label="Short name for this reference" help="Short names take less track space"> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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472 <sanitizer invalid_char="_"> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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473 <valid initial="string.printable"> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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474 <remove value="'"/> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit 1c04ea76330d0148a7682b3c26846e5a5df21f99
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475 </valid> |
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476 </sanitizer> |
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477 </param> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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478 </repeat> |
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479 </when> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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480 </conditional> |
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planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit aeef2fbc0f90a9366851941ff51baeba410c56e4
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481 </xml> |
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482 <xml name="citations"> |
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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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483 <citations> |
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484 <citation type="doi">10.1186/s13059-016-0924-1</citation> |
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485 <citation type="doi">10.1101/gr.094607.109</citation> |
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0
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486 </citations> |
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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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487 </xml> |
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488 </macros> |