Mercurial > repos > iuc > jbrowse
annotate jbrowse.xml @ 43:4542035c1075 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 55de003830db380639df997cdc5810df8022f63e"
| author | iuc |
|---|---|
| date | Tue, 16 Mar 2021 17:19:14 +0000 |
| parents | 6cd09d7b5f37 |
| children |
| rev | line source |
|---|---|
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8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
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1 <tool id="jbrowse" name="JBrowse" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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2 <description>genome browser</description> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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3 <macros> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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4 <import>macros.xml</import> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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5 </macros> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
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6 <xrefs> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
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7 <xref type="bio.tools">jbrowse</xref> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
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8 </xrefs> |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
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9 <expand macro="requirements"/> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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10 <edam_operations> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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11 <edam_operation>operation_0573</edam_operation> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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12 <edam_operation>operation_0564</edam_operation> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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13 </edam_operations> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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14 <edam_topics> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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15 <edam_topic>topic_3307</edam_topic> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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16 <edam_topic>topic_0092</edam_topic> |
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8774b28235bb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 8556ea066463f5e112b6ded2c1527011ab1e3b38"
iuc
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17 </edam_topics> |
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836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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18 <version_command>python '${__tool_directory__}/jbrowse.py' --version</version_command> |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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19 <command detect_errors="aggressive"><![CDATA[ |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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20 #if $action.action_select == "create": |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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21 mkdir -p $output.files_path && |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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22 #else: |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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23 cp -R $action.update_jbrowse.extra_files_path $output.files_path && |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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24 #end if |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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25 |
| 3 | 26 ## Copy the XML file into the directory, mostly for debugging |
| 27 ## but nice if users want to reproduce locally | |
| 28 cp $trackxml $output.files_path/galaxy.xml && | |
| 29 | |
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3235aeb45c22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
iuc
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30 export JBROWSE_SOURCE_DIR=\$(dirname \$(which prepare-refseqs.pl))/../opt/jbrowse && |
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3235aeb45c22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
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31 |
| 3 | 32 ## Once that's done, we run the python script to handle the real work |
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836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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33 python '$__tool_directory__/jbrowse.py' |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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34 |
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2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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35 --jbrowse \${JBROWSE_SOURCE_DIR} |
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17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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36 --standalone '$standalone' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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37 |
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ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
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38 --outdir $output.files_path |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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39 $trackxml && |
| 3 | 40 |
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17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
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41 #if str($standalone) != "data": |
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3235aeb45c22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
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42 cp $output.files_path/index.html $output; |
| 3 | 43 #else: |
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3235aeb45c22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
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44 cp $dummyIndex $output; |
| 3 | 45 #end if |
| 46 | |
| 47 ## Ugly testing hack since I cannot get <extra_files> to test the files I want to test. Hmph. | |
| 48 #if str($uglyTestingHack) == "enabled": | |
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3235aeb45c22
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 22ed9cb1e65cff5239df7ad4c76eaf0e981cf279"
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49 cp $trackxml $output |
| 3 | 50 #end if |
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5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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51 ]]></command> |
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497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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52 <configfiles> |
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5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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53 <configfile name="dummyIndex"><![CDATA[ |
| 3 | 54 <html> |
| 55 <head> | |
| 56 </head> | |
| 57 <body> | |
| 58 <h1>JBrowse Data Directory</h1> | |
| 59 <p> | |
| 60 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?) | |
| 61 started shipping with the ability to produce just the | |
| 62 "data" directory from a JBrowse instance, rather than a | |
| 63 complete, standalone instance. This was intended to be used | |
| 64 with the in-development Apollo integration, but may have other | |
| 65 uses as well. | |
| 66 </p> | |
| 67 <p> | |
| 68 <u>This is not usable on its own</u>. The output dataset may be | |
| 69 used with Apollo, or may be passed through the "JBrowse - | |
| 70 Convert to Standalone" tool in Galaxy to "upgrade" to a full | |
| 71 JBrowse instance. | |
| 72 </p> | |
| 73 </body> | |
| 74 </html> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
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75 ]]></configfile> |
| 3 | 76 <configfile name="trackxml"><![CDATA[<?xml version="1.0"?> |
| 77 <root> | |
| 78 <metadata> | |
| 79 <gencode>$gencode</gencode> | |
| 80 <genomes> | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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81 #if str($reference_genome.genome_type_select) == "indexed": |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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82 <genome path="${reference_genome.genomes.fields.path}"> |
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836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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83 <metadata /> |
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836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
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84 </genome>s |
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ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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85 #else |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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86 <genome path="$reference_genome.genome"> |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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87 <metadata> |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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88 <dataset id="${__app__.security.encode_id($reference_genome.genome.id)}" hid="${reference_genome.genome.hid}" |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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89 size="${reference_genome.genome.get_size(nice_size=True)}" |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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90 edam_format="${reference_genome.genome.datatype.edam_format}" |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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91 file_ext="${reference_genome.genome.ext}" /> |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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92 <history id="${__app__.security.encode_id($reference_genome.genome.history_id)}" |
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fd5dbf0f732e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da"
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93 #if $reference_genome.genome.history.user: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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94 user_email="${reference_genome.genome.history.user.email}" |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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95 user_id="${reference_genome.genome.history.user_id}" |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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96 display_name="${reference_genome.genome.history.get_display_name()}"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da"
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97 #else |
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fd5dbf0f732e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da"
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98 user_email="anonymous" |
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fd5dbf0f732e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da"
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99 user_id="-1" |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da"
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100 display_name="Unnamed History"/> |
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fd5dbf0f732e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 145eb8fdc1460af572d90991d048432f8e9582da"
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101 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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102 <metadata |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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103 #for (key, value) in $reference_genome.genome.get_metadata().items(): |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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104 #if "_types" not in $key: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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105 ${key}="${value}" |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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106 #end if |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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107 #end for |
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1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
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108 /> |
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1cfc579079a6
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109 <tool |
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110 tool_id="${reference_genome.genome.creating_job.tool_id}" |
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111 tool_version="${reference_genome.genome.creating_job.tool_version}" |
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112 /> |
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113 </metadata> |
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114 </genome> |
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115 #end if |
| 3 | 116 </genomes> |
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117 <general> |
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118 <defaultLocation>${jbgen.defaultLocation}</defaultLocation> |
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119 <trackPadding>${jbgen.trackPadding}</trackPadding> |
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120 |
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121 <shareLink>${jbgen.shareLink}</shareLink> |
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122 <aboutDescription>${jbgen.aboutDescription}</aboutDescription> |
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123 <show_tracklist>${jbgen.show_tracklist}</show_tracklist> |
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124 <show_nav>${jbgen.show_nav}</show_nav> |
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125 <show_overview>${jbgen.show_overview}</show_overview> |
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126 <show_menu>${jbgen.show_menu}</show_menu> |
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127 <hideGenomeOptions>${jbgen.hideGenomeOptions}</hideGenomeOptions> |
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128 </general> |
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129 <galaxyUrl>${__app__.config.galaxy_infrastructure_url}</galaxyUrl> |
| 3 | 130 </metadata> |
| 131 <tracks> | |
| 132 #for $tg in $track_groups: | |
| 133 #for $track in $tg.data_tracks: | |
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134 <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> |
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135 #if $track.data_format.data_format_select != "rest" and $track.data_format.data_format_select != "sparql": |
| 3 | 136 <files> |
| 137 #for $dataset in $track.data_format.annotation: | |
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138 <trackFile path="${dataset}" ext="${dataset.ext}" label="${dataset.element_identifier}"> |
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139 <metadata> |
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140 <dataset id="${__app__.security.encode_id($dataset.id)}" hid="${dataset.hid}" |
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141 size="${dataset.get_size(nice_size=True)}" |
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142 edam_format="${dataset.datatype.edam_format}" |
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143 file_ext="${dataset.ext}" /> |
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144 <history id="${__app__.security.encode_id($dataset.history_id)}" |
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145 #if $dataset.history.user: |
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146 user_email="${dataset.history.user.email}" |
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147 user_id="${dataset.history.user_id}" |
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148 display_name="${dataset.history.get_display_name()}"/> |
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149 #else |
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150 user_email="anonymous" |
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151 user_id="-1" |
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152 display_name="Unnamed History"/> |
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153 #end if |
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154 <metadata |
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155 #for (key, value) in $dataset.get_metadata().items(): |
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156 #if "_types" not in $key and $value is not None and len(str($value)) < 5000: |
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157 ${key}="${value}" |
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158 #end if |
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159 #end for |
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160 /> |
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161 <tool |
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162 tool_id="${dataset.creating_job.tool_id}" |
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163 tool_version="${dataset.creating_job.tool_version}" |
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164 /> |
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165 </metadata> |
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166 </trackFile> |
| 3 | 167 #end for |
| 168 </files> | |
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169 #end if |
| 3 | 170 |
| 171 <options> | |
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172 #if str($track.data_format.data_format_select) == "gene_calls" or str($track.data_format.data_format_select) == "blast" or str($track.data_format.data_format_select) == "rest" or str($track.data_format.data_format_select) == "sparql": |
| 3 | 173 <style> |
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174 <overridePlugins>${track.data_format.override_apollo_plugins}</overridePlugins> |
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175 <overrideDraggable>${track.data_format.override_apollo_drag}</overrideDraggable> |
| 3 | 176 <className>${track.data_format.jbstyle.style_classname}</className> |
| 177 <description>${track.data_format.jbstyle.style_description}</description> | |
| 178 <label>${track.data_format.jbstyle.style_label}</label> | |
| 179 <height>${track.data_format.jbstyle.style_height}</height> | |
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180 <maxHeight>${track.data_format.jbstyle.max_height}</maxHeight> |
| 3 | 181 </style> |
| 182 <scaling> | |
| 183 #if str($track.data_format.jbcolor_scale.color_score.color_score_select) == "none": | |
| 184 <method>ignore</method> | |
| 185 <scheme> | |
| 186 #if str($track.data_format.jbcolor_scale.color_score.color.color_select) == "automatic": | |
| 187 <color>__auto__</color> | |
| 188 #else | |
| 189 <color>${track.data_format.jbcolor_scale.color_score.color.style_color}</color> | |
| 190 #end if | |
| 191 </scheme> | |
| 192 #else | |
| 193 <method>score</method> | |
| 194 <algo>${track.data_format.jbcolor_scale.color_score.score_scaling}</algo> | |
| 195 <scales> | |
| 196 <type>${track.data_format.jbcolor_scale.color_score.score_scales.scale_select}</type> | |
| 197 | |
| 198 #if str($track.data_format.jbcolor_scale.color_score.score_scales.scale_select) == "manual": | |
| 199 <min>${track.data_format.jbcolor_scale.color_score.score_scales.minimum}</min> | |
| 200 <max>${track.data_format.jbcolor_scale.color_score.score_scales.maximum}</max> | |
| 201 #end if | |
| 202 </scales> | |
| 203 <scheme> | |
| 204 <type>${track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme}</type> | |
| 205 ## auto_color | |
| 206 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.score_scheme) == "opacity": | |
| 207 #if str($track.data_format.jbcolor_scale.color_score.color_scheme.color.color_select) == "automatic": | |
| 208 <color>__auto__</color> | |
| 209 #else | |
| 210 <color>${track.data_format.jbcolor_scale.color_score.color_scheme.color.style_color}</color> | |
| 211 #end if | |
| 212 #end if | |
| 213 </scheme> | |
| 214 #end if | |
| 215 </scaling> | |
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216 <menus> |
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217 #for $menu_item in $track.data_format.jbmenu.track_menu: |
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218 <menu> |
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219 <action>${menu_item.menu_action}</action> |
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220 #if str($menu_item.menu_label) != "": |
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221 <label>${menu_item.menu_label}</label> |
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222 #end if |
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223 #if str($menu_item.menu_title) != "": |
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224 <title>${menu_item.menu_title}</title> |
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225 #end if |
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226 #if str($menu_item.menu_url) != "": |
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227 <url>${menu_item.menu_url.replace("&", "&").replace("\"", """)}</url> |
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228 #end if |
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229 #if str($menu_item.menu_icon) != "": |
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230 <iconClass>${menu_item.menu_icon}</iconClass> |
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231 #end if |
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232 </menu> |
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233 #end for |
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234 </menus> |
| 3 | 235 #end if |
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236 #if str($track.data_format.data_format_select) in ["gene_calls", "pileup", "blast", "wiggle", "vcf"]: |
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237 <custom_config> |
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238 #for $custom_option in $track.data_format.jb_custom_config.option: |
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239 <${custom_option.opt_key}> |
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240 <${custom_option.opt_value.val_type}>${$custom_option.opt_value.val}</${custom_option.opt_value.val_type}> |
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241 </${custom_option.opt_key}> |
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242 #end for |
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243 </custom_config> |
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244 #end if |
| 3 | 245 |
| 246 #if str($track.data_format.data_format_select) == "wiggle": | |
| 247 <wiggle> | |
| 248 <type>${track.data_format.xyplot}</type> | |
| 249 <variance_band>${track.data_format.var_band}</variance_band> | |
| 250 #if str($track.data_format.scaling.scale_select) == "auto_local": | |
| 251 <autoscale>local</autoscale> | |
| 252 #else if str($track.data_format.scaling.scale_select) == "auto_global": | |
| 253 <autoscale>global</autoscale> | |
| 254 #else: | |
| 255 <min>${track.data_format.scaling.minimum}</min> | |
| 256 <max>${track.data_format.scaling.maximum}</max> | |
| 257 #end if | |
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258 <scale>${track.data_format.scale_select2}</scale> |
| 3 | 259 |
| 260 ## Wiggle tracks need special color config | |
| 261 #if str($track.data_format.jbcolor.color.color_select) != "automatic": | |
| 262 <color_pos>${track.data_format.jbcolor.color.style_pos_color}</color_pos> | |
| 263 <color_neg>${track.data_format.jbcolor.color.style_neg_color}</color_neg> | |
| 264 #else: | |
| 265 <color_pos>__auto__</color_pos> | |
| 266 <color_neg>__auto__</color_neg> | |
| 267 #end if | |
| 268 | |
| 269 ## Bicolor pivot config | |
| 270 #if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "zero": | |
| 271 <bicolor_pivot>zero</bicolor_pivot> | |
| 272 #else if str($track.data_format.jbcolor.bicolor_pivot.bicolor_pivot_select) == "mean": | |
| 273 <bicolor_pivot>mean</bicolor_pivot> | |
| 274 #else: | |
| 275 <bicolor_pivot>${track.data_format.jbcolor.bicolor_pivot.pivot_point}</bicolor_pivot> | |
| 276 #end if | |
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277 <multibigwig>${track.data_format.MultiBigWig}</multibigwig> |
| 3 | 278 </wiggle> |
| 279 #else if str($track.data_format.data_format_select) == "pileup": | |
| 280 <pileup> | |
| 281 <auto_snp>${track.data_format.auto_snp}</auto_snp> | |
| 282 <bam_indices> | |
| 283 #for $dataset in $track.data_format.annotation: | |
| 284 <bam_index>${dataset.metadata.bam_index}</bam_index> | |
| 285 #end for | |
| 286 </bam_indices> | |
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287 <chunkSizeLimit>${track.data_format.chunkSizeLimit}</chunkSizeLimit> |
| 3 | 288 </pileup> |
| 289 #else if str($track.data_format.data_format_select) == "blast": | |
| 290 <blast> | |
| 291 #if str($track.data_format.blast_parent) != "": | |
| 292 <parent>${track.data_format.blast_parent}</parent> | |
| 293 #end if | |
| 294 <protein>${track.data_format.is_protein}</protein> | |
| 295 <min_gap>${track.data_format.min_gap}</min_gap> | |
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296 <index>${track.data_format.index}</index> |
| 3 | 297 </blast> |
| 298 #else if str($track.data_format.data_format_select) == "gene_calls": | |
| 299 <gff> | |
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300 <trackType>${track.data_format.track_config.track_class}</trackType> |
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301 #if $track.data_format.track_config.track_class in ['JBrowse/View/Track/CanvasFeatures', 'NeatCanvasFeatures/View/Track/NeatFeatures']: |
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302 #if str($track.data_format.track_config.canvas_options.transcriptType) != "": |
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303 <transcriptType>${track.data_format.track_config.canvas_options.transcriptType}</transcriptType> |
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304 #end if |
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305 #if str($track.data_format.track_config.canvas_options.subParts) != "": |
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306 <subParts>${track.data_format.track_config.canvas_options.subParts}</subParts> |
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307 #end if |
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308 #if str($track.data_format.track_config.canvas_options.impliedUTRs) != "false": |
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309 <impliedUTRs>${track.data_format.track_config.canvas_options.impliedUTRs}</impliedUTRs> |
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310 #end if |
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311 #else if $track.data_format.track_config.track_class in ['JBrowse/View/Track/HTMLFeatures', 'NeatHTMLFeatures/View/Track/NeatFeatures']: |
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312 #if str($track.data_format.track_config.html_options.topLevelFeatures) != "": |
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313 <topLevelFeatures>${track.data_format.track_config.html_options.topLevelFeatures}</topLevelFeatures> |
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314 #end if |
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315 #end if |
| 3 | 316 #if $track.data_format.match_part.match_part_select: |
| 317 <match>${track.data_format.match_part.name}</match> | |
| 318 #end if | |
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319 <index>${track.data_format.index}</index> |
| 3 | 320 </gff> |
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321 #else if str($track.data_format.data_format_select) == "rest": |
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322 <label>${track.data_format.label}</label> |
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323 <rest> |
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324 <url>${track.data_format.url}</url> |
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325 </rest> |
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326 #else if str($track.data_format.data_format_select) == "sparql": |
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327 <label>${track.data_format.label}</label> |
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328 <sparql> |
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329 <url>${track.data_format.url}</url> |
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330 <query>${track.data_format.query}</query> |
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331 </sparql> |
| 3 | 332 #end if |
| 333 </options> | |
| 334 </track> | |
| 335 #end for | |
| 336 #end for | |
| 337 </tracks> | |
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338 ## Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed |
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339 ## <plugins |
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340 ## ComboTrackSelector="${plugins.ComboTrackSelector}" |
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341 ## Bookmarks="${plugins.Bookmarks}" |
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342 ## GCContent="${plugins.GCContent}" |
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343 ## BlastView="${plugins.BlastView}" |
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344 ## theme="${plugins.theme}" |
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345 ## /> |
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346 <plugins |
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347 ComboTrackSelector="${plugins.ComboTrackSelector}" |
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348 Bookmarks="" |
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349 GCContent="${plugins.GCContent}" |
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350 BlastView="${plugins.BlastView}" |
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351 theme="" |
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352 /> |
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353 </root> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
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354 ]]></configfile> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
355 </configfiles> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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diff
changeset
|
356 <inputs> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
357 <conditional name="reference_genome"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
358 <param help="Built-in references" label="Reference genome to display" name="genome_type_select" type="select"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
359 <option selected="True" value="indexed">Use a built-in genome</option> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
360 <option value="history">Use a genome from history</option> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
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diff
changeset
|
361 </param> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
362 <when value="indexed"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
363 <param |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
364 help="If your genome of interest is not listed, contact the Galaxy team" |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
365 label="Select a reference genome" |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
366 name="genomes" |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
367 type="select" |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
368 > |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
369 <options from_data_table="all_fasta"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
370 <filter column="2" type="sort_by" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
371 <validator message="No genomes are available for the selected input dataset" type="no_options" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
372 </options> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
373 </param> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
374 </when> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
375 <when value="history"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
376 <param |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
377 format="fasta" |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
378 label="Select the reference genome" |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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changeset
|
379 name="genome" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
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diff
changeset
|
380 type="data" /> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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changeset
|
381 </when> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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diff
changeset
|
382 </conditional> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
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changeset
|
383 |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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diff
changeset
|
384 <param name="standalone" label="Output JBrowse" type="select"> |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
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changeset
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385 <option value="complete">Complete, for viewing and further local development (JBrowse, tools, documentation, etc.)</option> |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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diff
changeset
|
386 <option value="minimal" selected="true">Minimal for viewing (Documentation removed)</option> |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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diff
changeset
|
387 <option value="data">Data directory only (primarily for use with Apollo, requires extra steps to serve as website)</option> |
|
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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diff
changeset
|
388 </param> |
| 3 | 389 |
|
22
5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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diff
changeset
|
390 <param name="gencode" type="select" label="Genetic Code"> |
| 3 | 391 <option value="1">1. The Standard Code</option> |
| 392 <option value="2">2. The Vertebrate Mitochondrial Code</option> | |
| 393 <option value="3">3. The Yeast Mitochondrial Code</option> | |
| 394 <option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
| 395 <option value="5">5. The Invertebrate Mitochondrial Code</option> | |
| 396 <option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
| 397 <option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option> | |
| 398 <option value="10">10. The Euplotid Nuclear Code</option> | |
| 399 <option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option> | |
| 400 <option value="12">12. The Alternative Yeast Nuclear Code</option> | |
| 401 <option value="13">13. The Ascidian Mitochondrial Code</option> | |
| 402 <option value="14">14. The Alternative Flatworm Mitochondrial Code</option> | |
| 403 <option value="16">16. Chlorophycean Mitochondrial Code</option> | |
| 404 <option value="21">21. Trematode Mitochondrial Code</option> | |
| 405 <option value="22">22. Scenedesmus obliquus Mitochondrial Code</option> | |
| 406 <option value="23">23. Thraustochytrium Mitochondrial Code</option> | |
| 407 <option value="24">24. Pterobranchia Mitochondrial Code</option> | |
| 408 <option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option> | |
| 409 </param> | |
| 410 | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
411 <conditional name="action"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
412 <param type="select" label="JBrowse-in-Galaxy Action" name="action_select"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
413 <option value="create">New JBrowse Instance</option> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
414 <option value="update">Update exising JBrowse Instance</option> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
415 </param> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
416 <when value="create" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
417 <when value="update"> |
|
22
5f70e7fe6077
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit a4b0969b33a68a0ea9ba12291f6694aec24f13ed
iuc
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changeset
|
418 <param name="update_jbrowse" type="data" format="html" label="Previous JBrowse Instance" /> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
419 </when> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
420 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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diff
changeset
|
421 |
| 3 | 422 <repeat name="track_groups" title="Track Group"> |
| 423 <param label="Track Category" | |
| 424 name="category" | |
| 425 type="text" | |
| 426 value="Default" | |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
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diff
changeset
|
427 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." optional="False"/> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
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changeset
|
428 <repeat name="data_tracks" title="Annotation Track"> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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diff
changeset
|
429 <conditional name="data_format" label="Track Options"> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
430 <param type="select" label="Track Type" name="data_format_select"> |
|
33
0ae74c70b267
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 369a727966d697c56633b27ad2757db40fef0dc3"
iuc
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diff
changeset
|
431 <option value="gene_calls">GFF/GFF3/BED Features</option> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
432 <option value="pileup">BAM Pileups</option> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
|
433 <option value="blast">Blast XML</option> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
434 <option value="wiggle">BigWig XY</option> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
435 <option value="vcf">VCF SNPs</option> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
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changeset
|
436 <option value="rest">REST Endpoint</option> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
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changeset
|
437 <option value="sparql">SPARQL</option> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
438 </param> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
439 <when value="blast"> |
| 3 | 440 <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
441 |
| 3 | 442 <param label="Features used in Blast Search" |
| 443 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." | |
| 444 format="gff3" | |
| 445 name="blast_parent" | |
| 446 optional="true" | |
| 447 type="data"/> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
|
448 |
| 3 | 449 <param label="Minimum Gap Size" |
| 450 help="before a new match_part feature is created" | |
| 451 name="min_gap" | |
| 452 type="integer" | |
| 453 value="10" | |
| 454 min="2" /> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
455 <param label="Is this a protein blast search?" |
| 3 | 456 type="boolean" |
| 457 name="is_protein" | |
| 458 truevalue="true" | |
| 459 falsevalue="false" /> | |
| 460 | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
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diff
changeset
|
461 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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parents:
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changeset
|
462 |
| 3 | 463 <expand macro="track_styling" |
| 464 classname="feature" | |
| 465 label="description" | |
| 466 description="Hit_titles" | |
| 467 height="600px"/> | |
| 468 <expand macro="color_selection" | |
| 469 token_scaling_lin_select="false" | |
| 470 token_scaling_log_select="true" /> | |
|
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2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
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changeset
|
471 <expand macro="track_custom_config" /> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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changeset
|
472 <expand macro="track_menu" /> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
473 <expand macro="track_display" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
474 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
475 <when value="vcf"> |
| 3 | 476 <expand macro="input_conditional" label="SNP Track Data" format="vcf" /> |
|
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
477 <expand macro="track_custom_config" /> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
478 <expand macro="track_display" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
479 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
480 <when value="gene_calls"> |
| 3 | 481 <expand macro="input_conditional" label="GFF/GFF3/BED Track Data" format="gff,gff3,bed" /> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
482 <conditional name="match_part" label="match/match_part data"> |
| 3 | 483 <param label="This is match/match_part data" |
| 484 type="boolean" | |
| 485 name="match_part_select" | |
| 486 truevalue="true" | |
| 487 falsevalue="false" /> | |
| 488 <when value="true"> | |
| 489 <param label="Match Part Feature Type" | |
| 490 name="name" | |
| 491 type="text" | |
| 492 value="match" | |
|
21
1c718d8b3532
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents:
19
diff
changeset
|
493 help="Match_parts have several 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)." |
|
1c718d8b3532
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9cac72c004cc7ef57be997e2fdafb3b1839a300f
iuc
parents:
19
diff
changeset
|
494 optional="True"/> |
| 3 | 495 </when> |
| 496 <when value="false" /> | |
| 497 </conditional> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
498 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
499 <param label="Index this track" name="index" type="boolean" checked="false" truevalue="true" falsevalue="false" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
500 |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
501 <conditional name="track_config"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
502 <param type="select" label="JBrowse Track Type [Advanced]" name="track_class"> |
|
26
08776ba76cf5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents:
25
diff
changeset
|
503 <option value="NeatHTMLFeatures/View/Track/NeatFeatures" selected="true">Neat HTML Features</option> |
|
08776ba76cf5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents:
25
diff
changeset
|
504 <option value="NeatCanvasFeatures/View/Track/NeatFeatures">Neat Canvas Features</option> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
505 <option value="JBrowse/View/Track/HTMLFeatures">HTML Features</option> |
|
26
08776ba76cf5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents:
25
diff
changeset
|
506 <option value="JBrowse/View/Track/CanvasFeatures">Canvas Features</option> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
507 <option value="BlastView/View/Track/CanvasFeatures">Blast Features</option><!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed --> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
508 </param> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
509 <when value="JBrowse/View/Track/CanvasFeatures"> |
|
27
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
510 <expand macro="canvas_options" /> |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
511 </when> |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
512 <when value="JBrowse/View/Track/HTMLFeatures"> |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
513 <expand macro="html_options" /> |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
514 </when> |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
515 <when value="BlastView/View/Track/CanvasFeatures" /> |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
516 <when value="NeatHTMLFeatures/View/Track/NeatFeatures"> |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
517 <expand macro="html_options" /> |
|
26
08776ba76cf5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 75f6e483debb4c0d388bf4a54df81ee89af598d5
iuc
parents:
25
diff
changeset
|
518 </when> |
|
27
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
519 <when value="NeatCanvasFeatures/View/Track/NeatFeatures"> |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
520 <expand macro="canvas_options" /> |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
521 </when> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
522 </conditional> |
|
27
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
523 <expand macro="track_styling" |
|
30
ca2def38369c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 74554507efb46fb40ce6e12f0b73425e52ec0977
iuc
parents:
29
diff
changeset
|
524 classname="feature" |
|
27
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
525 label="product,name,id" |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
526 description="note,description" |
|
61ce21e36cb5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0c51a106c04c2f56f5a172dd74c8494687870e46
iuc
parents:
26
diff
changeset
|
527 height="10px"/> |
| 3 | 528 <expand macro="color_selection" /> |
|
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
529 <expand macro="track_custom_config" /> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
530 <expand macro="track_menu" /> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
531 <expand macro="track_display" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
532 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
533 <when value="pileup"> |
| 3 | 534 <expand macro="input_conditional" label="BAM Track Data" format="bam" /> |
| 535 <param label="Autogenerate SNP Track" | |
| 536 help="Not recommended for deep coverage BAM files" | |
| 537 type="boolean" | |
| 538 name="auto_snp" | |
| 539 truevalue="true" | |
| 540 falsevalue="false" /> | |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
541 <param label="Maximum size of BAM chunks" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
542 name="chunkSizeLimit" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
543 type="integer" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
544 help="Maximum size in bytes of BAM chunks that the browser will try to deal with. When this is exceeded, most tracks will display 'Too much data' message." |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
545 value="5000000" /> |
|
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
546 <expand macro="track_custom_config" /> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
547 <expand macro="track_display" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
548 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
549 <when value="wiggle"> |
| 3 | 550 <expand macro="input_conditional" label="BigWig Track Data" format="bigwig" /> |
| 551 | |
| 552 <param label="Use XYPlot" | |
| 553 help="instead of continuous colored band" | |
| 554 type="boolean" | |
| 555 name="xyplot" | |
| 556 truevalue="JBrowse/View/Track/Wiggle/XYPlot" | |
| 557 falsevalue="JBrowse/View/Track/Wiggle/Density" /> | |
| 558 <param label="Show variance band" | |
| 559 help="Only for XYPlots" | |
| 560 type="boolean" | |
| 561 name="var_band" | |
| 562 truevalue="true" | |
| 563 falsevalue="false" /> | |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
564 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
565 <conditional name="scaling" label="Scaling"> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
566 <param type="select" label="Track Scaling" name="scale_select"> |
|
23
dba3c47e1798
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
iuc
parents:
22
diff
changeset
|
567 <option value="auto_local" selected="true">Autoscale (local)</option> |
|
dba3c47e1798
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit cf2c8f3039021b645ac45980a02ffe1f69a3f958
iuc
parents:
22
diff
changeset
|
568 <option value="auto_global">Autoscale (global)</option> |
| 3 | 569 <option value="fixed">Specify Min/Max</option> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
570 </param> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
571 <when value="auto_local"></when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
572 <when value="auto_global"></when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
573 <when value="fixed"> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
574 <param label="Track minimum" name="minimum" |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
575 type="integer" value="0" /> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
576 <param label="Track maximum" name="maximum" |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
577 type="integer" value="100" /> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
578 </when> |
|
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
579 </conditional> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
580 <param type="select" label="Visual Scaling" name="scale_select2"> |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
581 <option value="linear" selected="true">Linear</option> |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
582 <option value="log">Logarithmic (Dynamically Calculated)</option> |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
583 </param> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
584 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
585 <param label="Use MultiBigWig Plugin" name="MultiBigWig" truevalue="True" falsevalue="" type="boolean" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
586 help="MultiBigWig is a plugin to group multiple big-wig tracks in a more aesthetically pleasing format and to show data in a higher density display." /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
587 |
| 3 | 588 <expand macro="color_selection_minmax" /> |
|
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
589 <expand macro="track_custom_config" /> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
590 <expand macro="track_display" /> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
591 </when> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
592 <when value="rest"> |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
593 <param type="text" label="REST Endpoint" name="url" /> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
594 <param type="text" label="Track Label" name="label" value="REST Genes" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
595 <expand macro="track_styling" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
596 classname="feature" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
597 label="description" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
598 description="Hit_titles" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
599 height="600px"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
600 <expand macro="color_selection" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
601 token_scaling_lin_select="false" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
602 token_scaling_log_select="true" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
603 <expand macro="track_menu" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
604 <expand macro="track_display" /> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
605 </when> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
606 |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
607 <when value="sparql"> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
608 <param type="text" label="SPARQL Server URL" name="url" /> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
609 <param type="text" label="Track Label" name="label" value="SPARQL Genes" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
610 <param type="text" label="SPARQL Query" name="query" area="true"> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
611 <sanitizer> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
612 <mapping initial="galaxy.util.mapped_chars"> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
613 <add source=" " target=" " /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
614 <add source=">" target="__gt__" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
615 <add source="<" target="__lt__" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
616 </mapping> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
617 <valid initial="default"> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
618 <add value="|" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
619 <add value="#" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
620 <add value="{"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
621 <add value="}"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
622 <add value="!"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
623 <add value="?"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
624 <add value="&"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
625 <add value="+"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
626 <add value="="/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
627 <add value="'"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
628 <add value='"'/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
629 </valid> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
630 </sanitizer> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
631 </param> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
632 <expand macro="track_styling" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
633 classname="feature" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
634 label="description" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
635 description="Hit_titles" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
636 height="600px"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
637 <expand macro="color_selection" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
638 token_scaling_lin_select="false" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
639 token_scaling_log_select="true" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
640 <expand macro="track_menu" /> |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
641 <expand macro="track_display" /> |
|
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
642 </when> |
|
1
497c6bb3b717
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
0
diff
changeset
|
643 </conditional> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
644 </repeat> |
| 3 | 645 </repeat> |
| 646 | |
|
5
ae9382cfb6ac
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3bbca939ca8a3298a3a2d6450abb04a96851e1ed
iuc
parents:
3
diff
changeset
|
647 <expand macro="general_options" /> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
648 <!-- Disable plugins until https://github.com/GMOD/jbrowse/issues/1288 is fixed --> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
649 <section name="plugins" title="Plugins" expanded="false"> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
650 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
651 <param |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
652 label="BlastView" name="BlastView" truevalue="True" falsevalue="" type="boolean" checked="true" |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
653 help="A JBrowse plugin for viewing blast alignments. This plugin makes MANY assumptions about the format of your data, and may not work without those assumptions: 1) you use protein_match / match_part 2) your features have a Blast_qseq, Blast_mseq, and Blast_sseq attribute in their GFF3 representation." /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
654 |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
655 <param |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
656 label="Combo Track Selector" name="ComboTrackSelector" truevalue="True" falsevalue="" type="boolean" |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
657 help="ComboTrackSelector is a plugin to allow the co-existence of the Hierarchical and Faceted Track selectors in JBrowse, built for/by the Arabidopsis Information Portal (Araport) project" /> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
658 <!-- No way to disable now that it's built in jbrowse conda package --> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
659 <!--param |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
660 label="Bookmarks" name="Bookmarks" truevalue="True" falsevalue="" type="boolean" |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
661 help="JBrowse plugin allowing users to manage a persistent list of bookmarks kept in localstorage" /--> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
662 |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
663 <param |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
664 label="GC Content" name="GCContent" truevalue="True" falsevalue="" type="boolean" |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
665 help="A JBrowse plugin for plotting GC Content and GC Skew. The plugin consists of a storeClass that automatically calculates the percentage of G/C bases in a region, a track type that derives from the Wiggle XY or density types, and a dialog box to adjust the sliding window size, window step size, and the calculation mode (content or skew)." /> |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
666 |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
667 <!--param type="select" label="JBrowse Theme" name="theme"> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
668 <option value="" selected="True">Default</option> |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
669 <option value="Minimalist">Minimalist</option> |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
670 <option value="Dark">Dark</option> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
671 </param--> |
|
17
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
672 </section> |
|
ff11d442feed
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 908f16ea4eb082227437dc93e06e8cb742f5a257
iuc
parents:
16
diff
changeset
|
673 |
| 3 | 674 <param type="hidden" name="uglyTestingHack" value="" /> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
675 </inputs> |
|
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
676 <outputs> |
| 3 | 677 <data format="html" name="output" label="JBrowse on $on_string - $standalone"/> |
|
0
2c9e5136b416
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 685773d3da40afdc4d14846d4935b3b0a100f56e
iuc
parents:
diff
changeset
|
678 </outputs> |
| 3 | 679 <tests> |
| 680 <test> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
681 <param name="reference_genome|genome_type_select" value="history"/> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
682 <param name="reference_genome|genome" value="merlin.fa"/> |
| 3 | 683 <param name="gencode" value="1" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
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diff
changeset
|
684 <param name="standalone" value="data" /> |
| 3 | 685 <param name="uglyTestingHack" value="enabled" /> |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
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diff
changeset
|
686 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
687 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
688 <has_text text="<gencode>1</gencode>"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
689 <has_text text="genome path="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
690 <has_text text="dataset id="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
691 <has_text text="history id="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
692 <has_text text="metadata"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
693 <has_text text="tool_id"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
694 |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
695 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
696 </output> |
| 3 | 697 </test> |
| 698 <test> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
699 <param name="reference_genome|genome_type_select" value="history"/> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
700 <param name="reference_genome|genome" value="merlin.fa"/> |
| 3 | 701 <param name="gencode" value="11" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
39
diff
changeset
|
702 <param name="standalone" value="data" /> |
| 3 | 703 <param name="uglyTestingHack" value="enabled" /> |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
704 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
705 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
706 <has_text text="<gencode>11</gencode>"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
707 <has_text text="genome path="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
708 <has_text text="dataset id="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
709 <has_text text="history id="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
710 <has_text text="metadata"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
711 <has_text text="tool_id"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
712 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
713 </output> |
| 3 | 714 </test> |
| 715 <test> | |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
716 <param name="reference_genome|genome_type_select" value="history"/> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
717 <param name="reference_genome|genome" value="merlin.fa"/> |
| 3 | 718 <param name="gencode" value="11" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
39
diff
changeset
|
719 <param name="standalone" value="data" /> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
720 <repeat name="track_groups"> |
|
34
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
721 <param name="category" value="Default" /> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
722 <repeat name="data_tracks"> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
723 <conditional name="data_format"> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
724 <param name="data_format_select" value="gene_calls"/> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
725 <param name="annotation" value="bed/test-3.bed,bed/test-6.bed"/> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
726 </conditional> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
727 </repeat> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
728 </repeat> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
729 <param name="uglyTestingHack" value="enabled" /> |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
730 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
731 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
732 <has_text text="<gencode>11</gencode>"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
733 <has_text text="genome path="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
734 <has_text text="dataset id="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
735 <has_text text="history id="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
736 <has_text text="metadata"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
737 <has_text text="tool_id"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
738 <has_text text="trackFile path="></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
739 <has_text text="ext="bed" label="test-3.bed""></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
740 <has_text text="NeatHTMLFeatures"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
741 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
742 </output> |
|
34
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
743 </test> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
744 <test> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
745 <param name="reference_genome|genome_type_select" value="history"/> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
746 <param name="reference_genome|genome" value="merlin.fa"/> |
|
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
747 <param name="gencode" value="11" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
39
diff
changeset
|
748 <param name="standalone" value="data" /> |
|
34
9de82b4963e6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 0a26506563ff9b7fa683d3d0eaa16436c3560908"
iuc
parents:
33
diff
changeset
|
749 <repeat name="track_groups"> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
750 <param name="category" value="Auto Coloured" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
751 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
752 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
753 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
754 <param name="annotation" value="gff3/A.gff,gff3/B.gff,gff3/C.gff,gff3/D.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
755 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
756 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
757 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
758 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
759 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
760 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
761 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
762 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
763 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
764 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
765 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
766 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
767 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
768 </repeat> |
| 3 | 769 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
770 <repeat name="track_groups"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
771 <param name="category" value="Ignore Scale" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
772 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
773 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
774 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
775 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
776 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
777 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
778 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
779 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
780 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
781 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
782 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
783 <param name="color_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
784 <param name="style_color" value="#ff00ff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
785 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
786 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
787 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
788 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
789 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
790 </repeat> |
| 3 | 791 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
792 <repeat name="track_groups"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
793 <param name="category" value="Scaled Colour" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
794 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
795 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
796 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
797 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
798 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
799 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
800 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
801 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
802 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
803 <param name="color_score_select" value="score"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
804 <param name="score_scaling" value="linear"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
805 <conditional name="score_scales"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
806 <param name="scale_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
807 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
808 <conditional name="color_scheme"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
809 <param name="score_scheme" value="opacity"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
810 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
811 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
812 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
813 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
814 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
815 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
816 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
817 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
818 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
819 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
820 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
821 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
822 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
823 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
824 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
825 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
826 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
827 <param name="color_score_select" value="score"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
828 <param name="score_scaling" value="linear"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
829 <conditional name="score_scales"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
830 <param name="scale_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
831 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
832 <conditional name="color_scheme"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
833 <param name="score_scheme" value="opacity"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
834 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
835 <param name="color_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
836 <param name="style_color" value="#0000ff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
837 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
838 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
839 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
840 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
841 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
842 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
843 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
844 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
845 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
846 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
847 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
848 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
849 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
850 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
851 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
852 <param name="color_score_select" value="score"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
853 <param name="score_scaling" value="linear"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
854 <conditional name="score_scales"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
855 <param name="scale_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
856 <param name="minimum" value="0"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
857 <param name="maximum" value="1000"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
858 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
859 <conditional name="color_scheme"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
860 <param name="score_scheme" value="opacity"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
861 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
862 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
863 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
864 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
865 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
866 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
867 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
868 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
869 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
870 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
871 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
872 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
873 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
874 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
875 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
876 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
877 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
878 <param name="color_score_select" value="score"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
879 <param name="score_scaling" value="linear"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
880 <conditional name="score_scales"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
881 <param name="scale_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
882 <param name="minimum" value="0"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
883 <param name="maximum" value="1000"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
884 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
885 <conditional name="color_scheme"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
886 <param name="score_scheme" value="opacity"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
887 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
888 <param name="color_select" value="manual"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
889 <param name="style_color" value="#ff0000"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
890 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
891 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
892 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
893 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
894 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
895 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
896 </repeat> |
| 3 | 897 |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
898 <repeat name="track_groups"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
899 <param name="category" value="Realistic" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
900 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
901 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
902 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
903 <param name="annotation" value="gff3/interpro.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
904 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
905 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
906 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
907 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
908 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
909 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
910 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
911 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
912 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
913 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
914 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
915 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
916 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
917 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
918 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
919 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
920 <param name="annotation" value="gff3/2.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
921 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
922 <param name="match_part_select" value="true"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
923 <param name="name" value="cDNA_match"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
924 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
925 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
926 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
927 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
928 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
929 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
930 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
931 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
932 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
933 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
934 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
935 </repeat> |
| 3 | 936 |
| 937 <param name="uglyTestingHack" value="enabled" /> | |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
938 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
939 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
940 <has_text text="Auto Coloured"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
941 <has_text text="A.gff"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
942 <has_text text="B.gff"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
943 <has_text text="C.gff"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
944 <has_text text="D.gff"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
945 <has_text text="Scaled Colour"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
946 <has_text text="1.gff"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
947 <has_text text="2.gff"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
948 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
949 </output> |
| 3 | 950 </test> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
951 <test> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
952 <param name="reference_genome|genome_type_select" value="history"/> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
953 <param name="reference_genome|genome" value="merlin.fa"/> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
954 <param name="gencode" value="11" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
39
diff
changeset
|
955 <param name="standalone" value="data" /> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
956 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
957 <repeat name="track_groups"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
958 <param name="category" value="With menu or index" /> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
959 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
960 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
961 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
962 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
963 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
964 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
965 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
966 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
967 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
968 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
969 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
970 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
971 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
972 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
973 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
974 <section name="jbmenu"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
975 <repeat name="track_menu"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
976 <param name="menu_action" value="iframeDialog"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
977 <param name="menu_label" value="Some menu item"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
978 <param name="menu_title" value="Frame title"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
979 <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
980 <param name="menu_icon" value="dijitIconNewTask"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
981 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
982 <repeat name="track_menu"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
983 <param name="menu_action" value="newWindow"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
984 <param name="menu_label" value="Another menu item"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
985 <param name="menu_title" value="Frame title 2"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
986 <param name="menu_url" value="https://example.com/#!/?id={name}&q={type}&z="{end}""/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
987 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
988 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
989 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
990 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
991 <repeat name="data_tracks"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
992 <conditional name="data_format"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
993 <param name="data_format_select" value="gene_calls"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
994 <param name="annotation" value="gff3/1.gff"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
995 <param name="index" value="true"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
996 <conditional name="match_part"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
997 <param name="match_part_select" value="false"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
998 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
999 <section name="jbcolor_scale"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1000 <conditional name="color_score"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1001 <param name="color_score_select" value="none"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1002 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1003 <conditional name="color"> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1004 <param name="color_select" value="automatic"/> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1005 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1006 </section> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1007 </conditional> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1008 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1009 </repeat> |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1010 |
|
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1011 <param name="uglyTestingHack" value="enabled" /> |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1012 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1013 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1014 <has_text text="With menu or index"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1015 <has_text text="Some menu item"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1016 <has_text text="Frame title"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1017 <has_text text="dijitIconNewTask"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1018 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1019 </output> |
|
8
ad4b9d7eae6a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents:
6
diff
changeset
|
1020 </test> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1021 <test> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1022 <param name="reference_genome|genome_type_select" value="history"/> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1023 <param name="reference_genome|genome" value="merlin.fa"/> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1024 <param name="gencode" value="11" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
39
diff
changeset
|
1025 <param name="standalone" value="data" /> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1026 |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1027 <repeat name="track_groups"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1028 <param name="category" value="With canvas config" /> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1029 <repeat name="data_tracks"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1030 <conditional name="data_format"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1031 <param name="data_format_select" value="gene_calls"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1032 <param name="annotation" value="gff3/1.gff"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1033 <conditional name="match_part"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1034 <param name="match_part_select" value="false"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1035 </conditional> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1036 <conditional name="track_config"> |
|
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1037 <param name="track_class" value="JBrowse/View/Track/CanvasFeatures"/> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1038 <section name="canvas_options"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1039 <param name="transcriptType" value="transcript"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1040 <param name="subParts" value="exon"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1041 <param name="impliedUTRs" value="true"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1042 </section> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1043 </conditional> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1044 <section name="jbcolor_scale"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1045 <conditional name="color_score"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1046 <param name="color_score_select" value="none"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1047 </conditional> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1048 <conditional name="color"> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1049 <param name="color_select" value="automatic"/> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1050 </conditional> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1051 </section> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1052 </conditional> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1053 </repeat> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1054 </repeat> |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1055 |
|
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1056 <param name="uglyTestingHack" value="enabled" /> |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1057 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1058 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1059 <has_text text="With canvas config"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1060 <has_text text="<transcriptType>transcript</transcriptType>"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1061 <has_text text="<subParts>exon</subParts>"></has_text> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1062 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1063 </output> |
|
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1064 </test> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1065 <test> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1066 <param name="reference_genome|genome_type_select" value="history"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1067 <param name="reference_genome|genome" value="merlin.fa"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1068 <param name="gencode" value="11" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
39
diff
changeset
|
1069 <param name="standalone" value="data" /> |
|
31
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1070 |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1071 <repeat name="track_groups"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1072 <param name="category" value="With custom track config" /> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1073 <repeat name="data_tracks"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1074 <conditional name="data_format"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1075 <param name="data_format_select" value="gene_calls"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1076 <param name="annotation" value="gff3/1.gff"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1077 <conditional name="match_part"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1078 <param name="match_part_select" value="false"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1079 </conditional> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1080 <section name="jb_custom_config"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1081 <repeat name="option"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1082 <param name="opt_key" value="displayMode"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1083 <conditional name="opt_value"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1084 <param name="val_type" value="text"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1085 <param name="val" value="collapsed"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1086 </conditional> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1087 </repeat> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1088 <repeat name="option"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1089 <param name="opt_key" value="histograms.height"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1090 <conditional name="opt_value"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1091 <param name="val_type" value="integer"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1092 <param name="val" value="150"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1093 </conditional> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1094 </repeat> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1095 <repeat name="option"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1096 <param name="opt_key" value="maxFeatureScreenDensity"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1097 <conditional name="opt_value"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1098 <param name="val_type" value="float"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1099 <param name="val" value="0.1"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1100 </conditional> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1101 </repeat> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1102 <repeat name="option"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1103 <param name="opt_key" value="style.strandArrow"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1104 <conditional name="opt_value"> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1105 <param name="val_type" value="boolean"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1106 <param name="val" value="false"/> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1107 </conditional> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1108 </repeat> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1109 </section> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1110 </conditional> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1111 </repeat> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1112 </repeat> |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1113 |
|
2bb2e07a7a21
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 12dff0abf006f6c81f6462cdf4ea9c0c740d1e9c
iuc
parents:
30
diff
changeset
|
1114 <param name="uglyTestingHack" value="enabled" /> |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1115 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1116 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1117 <has_text text="1.gff"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1118 <has_text text="collapsed"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1119 <has_text text="150"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1120 <has_text text="maxFeatureScreenDensity"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1121 <has_text text="style.strandArrow"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1122 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1123 </output> |
|
10
1a6d882d340d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit ac44b067ee08de23180e8b5030374cf362ac4524
iuc
parents:
8
diff
changeset
|
1124 </test> |
|
18
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1125 <test> |
|
19
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1126 <param name="reference_genome|genome_type_select" value="history"/> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1127 <param name="reference_genome|genome" value="merlin.fa"/> |
|
19
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1128 <param name="gencode" value="11" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
39
diff
changeset
|
1129 <param name="standalone" value="data" /> |
|
19
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1130 |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1131 <repeat name="track_groups"> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1132 <param name="category" value="Auto Coloured" /> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1133 <repeat name="data_tracks"> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1134 <conditional name="data_format"> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1135 <param name="data_format_select" value="pileup"/> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1136 <param name="annotation" value="bam/merlin-sample.bam"/> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1137 </conditional> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1138 </repeat> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1139 </repeat> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1140 |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1141 <param name="uglyTestingHack" value="enabled" /> |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1142 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1143 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1144 <has_text text="merlin-sample.bam"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1145 <has_text text="sort_order="coordinate""/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1146 <has_text text="bam_index"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1147 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1148 </output> |
|
19
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1149 </test> |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1150 |
|
8f33c9fbc119
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 57eebdcb732acc74769bac72ab6bb3e9afd91f47
iuc
parents:
18
diff
changeset
|
1151 <test> |
|
18
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1152 <!-- data_table --> |
|
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1153 <param name="reference_genome|genome_type_select" value="indexed"/> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1154 <param name="reference_genome|genome" value="merlin"/> |
|
18
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1155 <param name="gencode" value="1" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
39
diff
changeset
|
1156 <param name="standalone" value="data" /> |
|
18
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1157 <param name="uglyTestingHack" value="enabled" /> |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1158 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1159 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1160 <has_text text="merlin.fa"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1161 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1162 </output> |
|
18
836d1aa3e89a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 3c41f2c44dd5080cbdb5f6bb85dac2b564c8966e
iuc
parents:
17
diff
changeset
|
1163 </test> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1164 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1165 <test> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1166 <param name="reference_genome|genome_type_select" value="history"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1167 <param name="reference_genome|genome" value="merlin.fa"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1168 <param name="gencode" value="11" /> |
|
40
17359b808b01
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2f072c4183a0d1221fb9d81909aeeafb2dbda892"
iuc
parents:
39
diff
changeset
|
1169 <param name="standalone" value="data" /> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1170 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1171 <repeat name="track_groups"> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1172 <param name="category" value="External endpoints" /> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1173 <repeat name="data_tracks"> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1174 <conditional name="data_format"> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1175 <param name="data_format_select" value="rest"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1176 <param name="url" value="http://example.org.external/rest_api/"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1177 <param name="label" value="Rest api"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1178 </conditional> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1179 </repeat> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1180 <repeat name="data_tracks"> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1181 <conditional name="data_format"> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1182 <param name="data_format_select" value="sparql"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1183 <param name="url" value="http://example.org.external/sparql/"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1184 <param name="label" value="Sparql endpoint"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1185 <param name="query" value=" DEFINE sql:select-option 'order' |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1186 prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1187 select ?start, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1188 ?end, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1189 IF( ?faldo_type = faldo:ForwardStrandPosition, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1190 1, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1191 IF( ?faldo_type = faldo:ReverseStrandPosition, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1192 -1, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1193 0 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1194 ) |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1195 ) as ?strand, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1196 str(?obj_type_name) as ?type, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1197 str(?label) as ?name, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1198 str(?obj_name) as ?description, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1199 ?obj as ?uniqueID, |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1200 ?parent as ?parentUniqueID |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1201 where { |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1202 values ?faldo_type { faldo:ForwardStrandPosition faldo:ReverseStrandPosition faldo:BothStrandsPosition } |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1203 }"/> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1204 </conditional> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1205 </repeat> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1206 </repeat> |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1207 |
|
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1208 <param name="uglyTestingHack" value="enabled" /> |
|
42
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1209 <output name="output"> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1210 <assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1211 <has_text text="http://example.org.external/sparql/"/> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1212 </assert_contents> |
|
6cd09d7b5f37
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 96f42b908d68ef8b1da5507e9216db74e46ebf06"
iuc
parents:
41
diff
changeset
|
1213 </output> |
|
25
1cfc579079a6
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit b6f9a87b6091cc881a49e0b6acfadc5e7786967f
iuc
parents:
23
diff
changeset
|
1214 </test> |
| 3 | 1215 </tests> |
|
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1216 <help><![CDATA[ |
| 3 | 1217 JBrowse-in-Galaxy |
| 1218 ================= | |
| 1219 | |
| 1220 JBrowse-in-Galaxy offers a highly configurable, workflow-compatible | |
| 1221 alternative to Trackster. | |
| 1222 | |
|
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1223 Overview |
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1224 -------- |
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1225 |
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1226 JBrowse is a fast, embeddable genome browser built completely with |
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1227 JavaScript and HTML5. |
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1228 |
| 3 | 1229 The JBrowse-in-Galaxy (JiG) tool was written to help build complex |
| 1230 JBrowse installations straight from Galaxy, taking advantage of the | |
| 1231 latest Galaxy features such as dataset collections, sections, and colour | |
| 1232 pickers. It allows you to build up a JBrowse instance without worrying | |
| 1233 about how to run the command line tools to format your data, and which | |
| 1234 options need to be supplied and where. Additionally it comes with many | |
| 1235 javascript functions to handle colouring of features which would be | |
| 1236 nearly impossible to write without the assistance of this tool. | |
| 1237 | |
|
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1238 The JBrowse-in-Galaxy tool is maintained by `the Galaxy IUC |
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1239 <https://github.com/galaxyproject/tools-iuc/issues>`__, who you can help you |
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1240 with missing features or bugs in the tool. |
| 3 | 1241 |
| 1242 Options | |
| 1243 ------- | |
| 1244 | |
| 1245 The first option you encounter is the **Fasta Sequence(s)**. This option | |
| 1246 now accepts multiple fasta files, allowing you to build JBrowse | |
| 1247 instances that contain data for multiple genomes or chrosomomes | |
| 1248 (generally known as "landmark features" in gff3 terminology.) Up to 30 | |
| 1249 will be shown from the dropdown selector within JBrowse, this is a known | |
| 1250 issue. | |
| 1251 | |
|
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1252 **Standalone Instances** enable you to have either a complete JBrowse instance |
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1253 in a dataset, or just the data directory without JBrowse (e.g. for Apollo). |
| 3 | 1254 Currently Galaxy copies the entire JBrowse directory in order to have a |
| 1255 complete, downloadable file that contains a ready-to-go JBrowse | |
| 1256 instance. This is obviously an anti-feature because users don't want a | |
|
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1257 complete copy of JBrowse (12Mb) that's duplicated for every JBrowse |
| 3 | 1258 dataset in their history, and admins don't want useless copies of |
| 1259 JBrowse on disk. Unfortunately we have not come up with the perfect | |
| 1260 solution just yet, but we're working on it! In the meantime, users have | |
| 1261 been given the option to produce just the ``data/`` directory. For those | |
| 1262 unfamiliar with JBrowse, the ``data/`` directory contains processed data | |
| 1263 files, but no way to view them. This feature is additionally implemented | |
| 1264 for upcoming `Apollo <https://github.com/gmod/apollo>`__ integration. | |
| 1265 | |
| 1266 **Genetic Code** is a new feature in v0.4 of JiG / v1.12.0 of JBrowse, | |
| 1267 which allows users to specify a non standard genetic code, and have | |
|
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1268 JBrowse highlight the correct start and stop codons. |
| 3 | 1269 |
| 1270 **Track Groups** represent a set of tracks in a single category. These | |
| 1271 can be used to let your users understand relationships between large | |
| 1272 groups of tracks. | |
| 1273 | |
| 1274 .. image:: sections.png | |
| 1275 | |
| 1276 Annotation Tracks | |
| 1277 ----------------- | |
| 1278 | |
| 1279 Within Track Groups, you have one or more **Annotation Tracks**. Each | |
| 1280 Annotation Track is a groups of datasets which have similar styling. | |
| 1281 This allows you to rapidly build up JBrowse instances without having to | |
| 1282 configure tracks individually. A massive improvement over previous | |
| 1283 versions. For example, if you have five different GFF3 files from | |
| 1284 various gene callers that you wish to display, you can take advantage of | |
| 1285 this feature to style all of them similarly. | |
| 1286 | |
| 1287 There are a few different types of tracks supported, each with their own | |
| 1288 set of options: | |
| 1289 | |
|
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1290 GFF3/BED |
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1291 ~~~~~~~~ |
| 3 | 1292 |
| 1293 These are your standard feature tracks. They usually highlight genes, | |
| 1294 mRNAs and other features of interest along a genomic region. The | |
| 1295 underlying tool and this help documentation focus primarily on GFF3 | |
| 1296 data, and have not been tested extensively with other formats. Automatic | |
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1297 min/max detection will fail under BED datasets. |
| 3 | 1298 |
| 1299 The data may be of a subclass we call **match/match part** data. This | |
| 1300 consists of top level ``match`` features, with a child ``match_part`` | |
| 1301 feature, and is often used in displaying alignments. (See "Alignments" | |
| 1302 section on the `GFF3 | |
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1303 specification <https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md>`__ for more |
| 3 | 1304 information). If the data is match/match part, you will need to specify |
| 1305 the top level match feature name, as it can be one of a few different SO | |
| 1306 terms, and JiG does not yet have the ability to understand SO terms. | |
| 1307 | |
| 1308 Next up is the **Styling Options** section, which lets you control a few | |
| 1309 properties on how the track is styled. Most of these you will not need | |
| 1310 to configure and can safely leave on defaults. Occasionally you will | |
| 1311 want to change what information is shown in the end product. | |
| 1312 | |
| 1313 .. image:: styling.png | |
| 1314 | |
| 1315 In the above image you can see some black text, and some blue text. The | |
| 1316 source of the black text is configured with the **style.label** option, | |
| 1317 and the source of the blue text is configured with the | |
| 1318 **style.description** option. | |
| 1319 | |
| 1320 Feature Score Scaling & Colouring Options | |
| 1321 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 1322 | |
| 1323 First, you need to choose between ignoring the score attribute of GFF3 | |
| 1324 files, or using it. If you choose to ignore it, all features will be | |
| 1325 coloured with a solid colour. If you choose to use it, features will | |
| 1326 have slightly different colours based on their scores. | |
| 1327 | |
| 1328 .. image:: opacity.png | |
| 1329 | |
| 1330 If you choose **Ignore score**, you may choose between automatically | |
| 1331 choosing a colour, or manually specifying one. The automatically chosen | |
| 1332 colours vary along a brewer palette and generally look quite nice with | |
| 1333 no human intervention required. The manual colour choice is somewhat | |
| 1334 self explanatory. Clicking on the small coloured square will bring up a | |
| 1335 colour palette. | |
| 1336 | |
| 1337 If you choose **Base on score**, you're faced with a dizzying array of | |
| 1338 options. First is the function to map the colour choices to colour | |
| 1339 values. JiG comes with a few functions built in such as linear scaling, | |
| 1340 logarithmic scaling, and blast scaling. | |
| 1341 | |
| 1342 The **linear scaling** method says "take these values, and they map | |
| 1343 directly to a range of output values". **Logarithmic scaling** says | |
| 1344 "please take the log of the score before mapping", and **Blast scaling** | |
| 1345 is further specialised to handle blast data more nicely. These are | |
| 1346 convenience functions to help transform the wide array of possible | |
| 1347 values in the GFF3 score attribute to more meaningful numbers. If you | |
| 1348 need more comprehensive score scaling, it is recommended that you | |
| 1349 pre-process your GFF3 files somehow. | |
| 1350 | |
| 1351 Once you've selected a scaling method, you can choose to manually | |
| 1352 specify the minimum and maximum expected values, or you can let JiG | |
| 1353 determine them for you automatically. | |
| 1354 | |
| 1355 Finally, opacity is the only mapping we currently provide. Future | |
| 1356 iterations will attempt to improve upon this and provide more colour | |
| 1357 scales. The Opacity option maps the highest scoring features to full | |
| 1358 opacity, and everything else to lower ones. | |
| 1359 | |
| 1360 BAM Pileups | |
| 1361 ~~~~~~~~~~~ | |
| 1362 | |
| 1363 We support BAM files and can automatically generate SNP tracks based on | |
| 1364 that bam data. | |
| 1365 | |
| 1366 .. image:: bam.png | |
| 1367 | |
| 1368 This is *strongly discouraged* for high coverage density datasets. | |
| 1369 Unfortunately there are no other configuration options exposed for bam | |
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1370 files. |
| 3 | 1371 |
| 1372 BlastXML | |
| 1373 ~~~~~~~~ | |
| 1374 | |
| 1375 .. image:: blast.png | |
| 1376 | |
| 1377 JiG now supports both blastn and blastp datasets. JiG internally uses a | |
| 1378 blastXML to gapped GFF3 tool to convert your blastxml datasets into a | |
| 1379 format amenable to visualization in JBrowse. This tool is also | |
| 1380 available separately from the IUC on the toolshed. | |
| 1381 | |
| 1382 **Minimum Gap Size** reflects how long a gap must be before it becomes a | |
| 1383 real gap in the processed gff3 file. In the picture above, various sizes | |
| 1384 of gaps can be seen. If the minimum gap size was set much higher, say | |
| 1385 100nt, many of the smaller gaps would disappear, and the features on | |
| 1386 both sides would be merged into one, longer feature. This setting is | |
| 1387 inversely proportional to runtime and output file size. *Do not set this | |
| 1388 to a low value for large datasets*. By setting this number lower, you | |
| 1389 will have extremely large outputs and extremely long runtimes. The | |
| 1390 default was configured based off of the author's experience, but the | |
| 1391 author only works on small viruses. It is *strongly* recommended that | |
| 1392 you filter your blast results before display, e.g. picking out the top | |
| 1393 10 hits or so. | |
| 1394 | |
| 1395 **Protein blast search** option merely informs underlying tools that | |
| 1396 they should adjust feature locations by 3x. | |
| 1397 | |
| 1398 Styling Options | |
| 1399 ^^^^^^^^^^^^^^^ | |
| 1400 | |
| 1401 Please see the styling options for GFF3 datasets, they are identical. | |
| 1402 | |
| 1403 Feature Score Scaling & Coloring Options | |
| 1404 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | |
| 1405 | |
| 1406 Please see the score scaling and colouring options for GFF3 datasets, | |
| 1407 they are identical. Remember to set your score scaling to "blast" method | |
| 1408 if you do use it. | |
| 1409 | |
| 1410 Bigwig XY | |
| 1411 ~~~~~~~~~ | |
| 1412 | |
| 1413 .. image:: bigwig.png | |
| 1414 | |
| 1415 **XYPlot** | |
| 1416 | |
| 1417 BigWig tracks can be displayed as a "density" plot which is continuous | |
| 1418 line which varies in colour, or as an "XYplot." XYplots are preferable | |
| 1419 for users to visually identify specific features in a bigwig track, | |
| 1420 however density tracks are more visually compact. | |
| 1421 | |
| 1422 **Variance Band** is an option available to XYPlots, and can be seen in | |
| 1423 the third and fourth tracks in the above picture. This overlays a mean | |
| 1424 line, and 1 and 2 standard deviation areas. | |
| 1425 | |
| 1426 **Track Scaling** is different from colour scaling, instead it | |
| 1427 configures how the track behaves inside of JBrowse. **Autoscaling | |
| 1428 globally** means that JBrowse will determine the minimum and maximum for | |
| 1429 the track, and fix the bounds of the viewport to that. E.g. if your | |
| 1430 track ranges from 1-1000, and the region you're currently zoomed to only | |
| 1431 goes from 0-50, then the viewport range will still show 1-1000. This is | |
| 1432 good for global genomic context. However you may wish to consider | |
| 1433 **autoscaling locally** instead. In the example of a region which varies | |
| 1434 from 0-50, autoscaling locally would cause the individual track's | |
| 1435 viewport to re-adjust and show just the 0-50 region. If neither of these | |
| 1436 options are palatable, you may manually hardcode the minimum and | |
| 1437 maximums for the track to scale to. | |
| 1438 | |
| 1439 Colour Options | |
| 1440 ^^^^^^^^^^^^^^ | |
| 1441 | |
| 1442 BigWig tracks have two colours in JBrowse, a positive and a negative | |
| 1443 colour. | |
| 1444 | |
| 1445 As always you may manually choose a colour, or let JiG choose for you. | |
| 1446 | |
| 1447 One of the more interesting options is the **Bicolor pivot**. This | |
| 1448 option allows you to control the point at which JBrowse switches from | |
| 1449 the positive colour to the negative. In the above graphic, you can see | |
| 1450 this has been configured to "mean" for the first two (orange and blue) | |
| 1451 tracks. | |
| 1452 | |
| 1453 VCFs/SNPs | |
| 1454 ~~~~~~~~~ | |
| 1455 | |
| 1456 These tracks do not support any special configuration. | |
| 1457 | |
| 1458 Known Issues | |
| 1459 ------------ | |
| 1460 | |
| 1461 - More than 30 landmark features cannot be listed in the manual | |
| 1462 selector. | |
| 1463 - Non GFF3 likely has issue with automatically determined min/max | |
| 1464 scores. Manually specify minimum and maximum score attributes, or do | |
| 1465 not use varied colours based on scores to avoid this issue. | |
| 1466 | |
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1467 @ATTRIBUTION@ |
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1468 ]]></help> |
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1469 <expand macro="citations"/> |
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1470 </tool> |