Mercurial > repos > gga > apollo_fetch_jbrowse
comparison fetch_organism_jbrowse.xml @ 5:1a2976c6b161 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
| author | gga |
|---|---|
| date | Fri, 31 Aug 2018 09:33:16 -0400 |
| parents | 9968eec7430e |
| children | d8bb1f9b85b2 |
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| 4:9968eec7430e | 5:1a2976c6b161 |
|---|---|
| 13 | 13 |
| 14 python $__tool_directory__/fetch_organism_jbrowse.py | 14 python $__tool_directory__/fetch_organism_jbrowse.py |
| 15 @ADMIN_AUTH@ | 15 @ADMIN_AUTH@ |
| 16 | 16 |
| 17 @ORG_OR_GUESS@ | 17 @ORG_OR_GUESS@ |
| 18 $jbrowse.files_path/ && | 18 $jbrowse.files_path/ |
| 19 | |
| 20 "$__user_email__" && | |
| 19 | 21 |
| 20 cp $dummyIndex $jbrowse && | 22 cp $dummyIndex $jbrowse && |
| 21 find $jbrowse.files_path -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse && | 23 find $jbrowse.files_path -type f -printf '<li><a href="%P">%P</a></li>\n' | sort >> $jbrowse && |
| 22 echo '</ul></body></html>' >> $jbrowse | 24 echo '</ul></body></html>' >> $jbrowse |
| 23 | 25 |
| 54 </configfiles> | 56 </configfiles> |
| 55 <inputs> | 57 <inputs> |
| 56 <expand macro="org_or_guess" /> | 58 <expand macro="org_or_guess" /> |
| 57 </inputs> | 59 </inputs> |
| 58 <outputs> | 60 <outputs> |
| 59 <data format="html" name="jbrowse"/> | 61 <data format="html" name="jbrowse"> |
| 62 <discover_datasets pattern="(?P<designation>.+)\.txt" format="tabular" visible="true"/> | |
| 63 </data> | |
| 60 </outputs> | 64 </outputs> |
| 61 <tests> | 65 <tests> |
| 62 <test expect_failure="true"> | 66 <test expect_failure="true"> |
| 63 <conditional name="org_source"> | 67 <conditional name="org_source"> |
| 64 <param name="source_select" value="direct"/> | 68 <param name="source_select" value="direct"/> |