Mercurial > repos > gga > apollo_fetch_jbrowse
comparison fetch_organism_jbrowse.xml @ 0:c6d7f19953a6 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
| author | gga |
|---|---|
| date | Mon, 11 Sep 2017 05:47:25 -0400 |
| parents | |
| children | 9968eec7430e |
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| -1:000000000000 | 0:c6d7f19953a6 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="fetch_jbrowse" name="Retrieve JBrowse" version="3.2" profile="16.04"> | |
| 3 <description>for an organism, from Apollo</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <code file="webapollo.py"/> | |
| 9 <command detect_errors="aggressive"><![CDATA[ | |
| 10 mkdir -p $jbrowse.files_path/ | |
| 11 | |
| 12 && | |
| 13 | |
| 14 python $__tool_directory__/fetch_organism_jbrowse.py | |
| 15 @ADMIN_AUTH@ | |
| 16 | |
| 17 @ORG_OR_GUESS@ | |
| 18 $jbrowse.files_path/ && | |
| 19 | |
| 20 cp $dummyIndex $jbrowse && | |
| 21 find $jbrowse.files_path -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse && | |
| 22 echo '</ul></body></html>' >> $jbrowse | |
| 23 | |
| 24 ]]></command> | |
| 25 <configfiles> | |
| 26 <configfile name="dummyIndex"> | |
| 27 <![CDATA[ | |
| 28 <html> | |
| 29 <head> | |
| 30 </head> | |
| 31 <body> | |
| 32 <h1>JBrowse Data Directory</h1> | |
| 33 <p> | |
| 34 Hi! This is not a full JBrowse instance. JBrowse v0.4(+?) | |
| 35 started shipping with the ability to produce just the | |
| 36 "data" directory from a JBrowse instance, rather than a | |
| 37 complete, standalone instance. This was intended to be used | |
| 38 with the in-development Apollo integration, but may have other | |
| 39 uses as well. | |
| 40 </p> | |
| 41 <p> | |
| 42 <u>This is not usable on its own</u>. The output dataset may be | |
| 43 used with Apollo, or may be passed through the "JBrowse - | |
| 44 Convert to Standalone" tool in Galaxy to "upgrade" to a full | |
| 45 JBrowse instance. | |
| 46 </p> | |
| 47 <p> | |
| 48 The following list is provided for your convenience / debugging. | |
| 49 </p> | |
| 50 <h2>Contained Files</h2> | |
| 51 <ul> | |
| 52 ]]> | |
| 53 </configfile> | |
| 54 </configfiles> | |
| 55 <inputs> | |
| 56 <expand macro="org_or_guess" /> | |
| 57 </inputs> | |
| 58 <outputs> | |
| 59 <data format="html" name="jbrowse"/> | |
| 60 </outputs> | |
| 61 <tests> | |
| 62 <test expect_failure="true"> | |
| 63 <conditional name="org_source"> | |
| 64 <param name="source_select" value="direct"/> | |
| 65 <param name="org_raw" value="Test org" /> | |
| 66 </conditional> | |
| 67 <expand macro="test_result" /> | |
| 68 </test> | |
| 69 </tests> | |
| 70 <help><![CDATA[ | |
| 71 **What it does** | |
| 72 | |
| 73 Fetches the JBrowse directory from Apollo back into Galaxy. | |
| 74 | |
| 75 .. class:: warningmark | |
| 76 | |
| 77 If you provide an Apollo JSON file, only the first organism block will be used | |
| 78 in Common Name determination, as it is improbable you wish to apply a single | |
| 79 JBrowse instance to multiple organisms. | |
| 80 | |
| 81 @REFERENCES@ | |
| 82 ]]></help> | |
| 83 <expand macro="citations"/> | |
| 84 </tool> |