| Previous changeset 112:56f9a6e0fe80 (2024-07-04) Next changeset 114:75f01bd05bd8 (2024-08-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 45375b64cbc99173525a2b374d71a13e650ce1b0 |
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modified:
autogenJB2.py jbrowse2.xml macros.xml |
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| diff -r 56f9a6e0fe80 -r 878c27dfea9d autogenJB2.py --- a/autogenJB2.py Thu Jul 04 08:40:21 2024 +0000 +++ b/autogenJB2.py Sun Jul 28 02:42:43 2024 +0000 |
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| @@ -92,6 +92,11 @@ # foo.paf must have a foo_paf.fasta or fasta.gz to match tnames = [x[2] for x in listtracks] texts = [x[1] for x in listtracks] + if len(listtracks) == 0: + sys.stderr.write( + "Please add at least one track (bam,bed,bigwig,blastxml,cram,gff,hic,maf,paf or vcf) to the collection. No suitable track files for autogenJB2 - nothing to process" + ) + sys.exit(5) for i, track in enumerate(listtracks): track_conf = { "trackfiles": [], @@ -224,5 +229,5 @@ # jc.text_index() not sure what broke here. else: sys.stderr.write( - "Collection has no suitable trackfiles for autogenJB2 - nothing to process" + "Please add a fasta genome reference to the collection. No suitable reference fasta for autogenJB2 - nothing to process" ) |
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| diff -r 56f9a6e0fe80 -r 878c27dfea9d jbrowse2.xml --- a/jbrowse2.xml Thu Jul 04 08:40:21 2024 +0000 +++ b/jbrowse2.xml Sun Jul 28 02:42:43 2024 +0000 |
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| @@ -5,7 +5,7 @@ </macros> <expand macro="edamInc"/> <xrefs> - <xref type="bio.tools">jbrowse2</xref> + <xref type="bio.tools">jbrowse_2</xref> </xrefs> <expand macro="requirements"/> <required_files> |
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| diff -r 56f9a6e0fe80 -r 878c27dfea9d macros.xml --- a/macros.xml Thu Jul 04 08:40:21 2024 +0000 +++ b/macros.xml Sun Jul 28 02:42:43 2024 +0000 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@TOOL_VERSION@">2.12.3</token> + <token name="@TOOL_VERSION@">2.13.0</token> <xml name="edamInc"> <edam_topics> <edam_topic>topic_3307</edam_topic> |