| Previous changeset 35:259891fce7fd (2017-08-09) Next changeset 37:eeeb21870a73 (2018-05-31) |
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Commit message:
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit 9526de68e38a82bb84b2d9267a8c290c6adcaa65 |
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modified:
tools/mira4_0/README.rst tools/mira4_0/mira4_de_novo.xml tools/mira4_0/repository_dependencies.xml |
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| diff -r 259891fce7fd -r 46d73b942b43 tools/mira4_0/README.rst --- a/tools/mira4_0/README.rst Wed Aug 09 13:32:11 2017 -0400 +++ b/tools/mira4_0/README.rst Fri Sep 15 10:09:14 2017 -0400 |
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| @@ -9,7 +9,7 @@ to where Galaxy expects the files) and associated Galaxy wrapper XML file. It is available from the Galaxy Tool Shed at: -http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler +http://toolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler It uses a Galaxy datatype definition 'mira' for the MIRA Assembly Format, http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes @@ -38,7 +38,7 @@ First install the 'mira' datatype for Galaxy, available here: -* http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes +* http://toolshed.g2.bx.psu.edu/view/peterjc/mira_datatypes There are various Python and XML files to install into Galaxy: @@ -138,7 +138,7 @@ $ planemo shed_upload --tar_only tools/mira4_0/ ... - $ tar -tzf shed_upload.tar.gz + $ tar -tzf shed_upload.tar.gz test-data/U13small_m.fastq ... |
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| diff -r 259891fce7fd -r 46d73b942b43 tools/mira4_0/mira4_de_novo.xml --- a/tools/mira4_0/mira4_de_novo.xml Wed Aug 09 13:32:11 2017 -0400 +++ b/tools/mira4_0/mira4_de_novo.xml Fri Sep 15 10:09:14 2017 -0400 |
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| @@ -38,7 +38,7 @@ ## point to a local hard drive (not something like NFS on network). ## We replace /tmp with an environment variable via mira4.py ## -## -OUT:orc=no is short for -OUTPUT:output_result_caf=no +## -OUT:orc=no is short for -OUTPUT:output_result_caf=no ## which turns off an output file we don't want anyway. #for $rg in $read_group @@ -142,8 +142,8 @@ <data name="out_maf" format="mira" label="MIRA de novo assembly"> <filter>maf_wanted is True</filter> </data> - <!-- TODO? - <data name="out_contigstats" format="tabular" label="MIRA contig stats" /> + <!-- TODO? + <data name="out_contigstats" format="tabular" label="MIRA contig stats" /> --> <data name="out_log" format="txt" label="MIRA de novo log" /> </outputs> |
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| diff -r 259891fce7fd -r 46d73b942b43 tools/mira4_0/repository_dependencies.xml --- a/tools/mira4_0/repository_dependencies.xml Wed Aug 09 13:32:11 2017 -0400 +++ b/tools/mira4_0/repository_dependencies.xml Fri Sep 15 10:09:14 2017 -0400 |
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| @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the MIRA datatype definitions (e.g. the MIRA Assembly Format)."> - <repository changeset_revision="f4d34bd3c633" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="34c6c83bf215" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories> |