Mercurial > repos > fubar > jbrowse2
diff jbrowse2.xml @ 38:07849bf248e3 draft
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit a74e469a81b38c7142f63de510ae31d3754d1767
| author | fubar |
|---|---|
| date | Fri, 01 Mar 2024 00:40:38 +0000 |
| parents | 5f39f745682f |
| children | e1a3d3221ed3 |
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--- a/jbrowse2.xml Thu Feb 29 00:51:45 2024 +0000 +++ b/jbrowse2.xml Fri Mar 01 00:40:38 2024 +0000 @@ -14,7 +14,12 @@ ## Copy the XML file into the directory, mostly for debugging ## but nice if users want to reproduce locally cp '$trackxml' '$output.files_path/galaxy.xml' && + +export JBROWSE2_PATH=\$(dirname \$(which jbrowse))/../opt/jbrowse2 && + +## Once that's done, we run the python script to handle the real work python '$__tool_directory__/jbrowse2.py' +--jbrowse2path \${JBROWSE2_PATH} --outdir '$output.files_path' --xml '$trackxml' && #if $jbgen.zipOut == "true": @@ -356,7 +361,7 @@ <param name="category" value="Default" /> <repeat name="data_tracks"> <conditional name="data_format"> - <param name="data_format_select" value="wiggle"/> + <param name="data_format_select" value="bigwig"/> <param name="annotation" value="bw/merlin.bw"/> </conditional> </repeat> @@ -371,11 +376,10 @@ <has_text text="tool_id"></has_text> <has_text text="trackFile path="></has_text> <has_text text="file_ext="bigwig""></has_text> - <has_text text="format="wiggle""></has_text> + <has_text text="format="bigwig""></has_text> </assert_contents> </output> </test> - <test> <param name="reference_genome|genome_type_select" value="history"/> <param name="reference_genome|genome" value="merlin.fa"/> @@ -710,7 +714,6 @@ </assert_contents> </output> </test> - <!-- TODO add a synteny test --> <!-- TODO add a bam and a cram test --> <!-- TODO add an hic test -->