Mercurial > repos > devteam > kraken
changeset 8:8ba2174315aa draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit 87dfa1af2f1dd57ffc7290b66218a127cec6757f
| author | iuc |
|---|---|
| date | Mon, 14 Jan 2019 16:48:56 -0500 |
| parents | 658d47fd33e3 |
| children | aec58624706f |
| files | kraken.xml macros.xml test-data/test_database.loc tool-data/kraken_databases.loc.sample |
| diffstat | 4 files changed, 55 insertions(+), 6 deletions(-) [+] |
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--- a/kraken.xml Thu Sep 13 09:44:31 2018 -0400 +++ b/kraken.xml Mon Jan 14 16:48:56 2019 -0500 @@ -116,8 +116,16 @@ <param name="split_reads" value="false"/> <param name="quick" value="no"/> <param name="only-classified-output" value="false"/> - <param name="kraken_database" value="test_db"/> - + <param name="kraken_database" value="old_style_test_entry"/> + <output name="output" file="kraken_test1_output.tab" ftype="tabular"/> + </test> + <test> + <param name="single_paired_selector" value="no"/> + <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/> + <param name="split_reads" value="false"/> + <param name="quick" value="no"/> + <param name="only-classified-output" value="false"/> + <param name="kraken_database" value="new_style_test_entry"/> <output name="output" file="kraken_test1_output.tab" ftype="tabular"/> </test> </tests>
--- a/macros.xml Thu Sep 13 09:44:31 2018 -0400 +++ b/macros.xml Mon Jan 14 16:48:56 2019 -0500 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@WRAPPER_VERSION@">1.2.4</token> + <token name="@WRAPPER_VERSION@">1.3.0</token> <xml name="requirements"> <requirements> <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement> @@ -23,6 +23,10 @@ <citation type="doi">10.1186/gb-2014-15-3-r46</citation> </citations> </xml> - <token name="@INPUT_DATABASE@">--db '${kraken_database.fields.name}'</token> - <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH='${kraken_database.fields.path}'</token> + <!-- See the kraken_databases.loc.sample documentation, + this if statement is for backward compatibility as early + versions of the wrapper assumed the UI facing field name + was also part of the directory path --> + <token name="@SET_DATABASE_PATH@">if [ -d '${kraken_database.fields.path}/${kraken_database.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}/${kraken_database.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_database.fields.path}'; fi</token> + <token name="@INPUT_DATABASE@">--db "\$KRAKEN_DEFAULT_DB"</token> </macros>
--- a/test-data/test_database.loc Thu Sep 13 09:44:31 2018 -0400 +++ b/test-data/test_database.loc Mon Jan 14 16:48:56 2019 -0500 @@ -1,1 +1,20 @@ -test_db test_db ${__HERE__} \ No newline at end of file +# Tab separated with three columns: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the Kraken DB) +# +# Modern usage assumes $path is the folder containing +# the Kraken database of interest: +# +new_style_test_entry "Test Database" ${__HERE__}/test_db + +# The kraken wrapper still supports an alternative +# legacy usage where $path/$name is the folder +# containing the Kraken database of interest, meaning +# $name must be both a folder name and human readable +# description of the DB to show in the Galaxy UI: +old_style_test_entry test_db ${__HERE__} + +# NOTE: This legacy style should be avoided as other +# tools also using the kraken_database.loc file may +# not understand it!
--- a/tool-data/kraken_databases.loc.sample Thu Sep 13 09:44:31 2018 -0400 +++ b/tool-data/kraken_databases.loc.sample Mon Jan 14 16:48:56 2019 -0500 @@ -0,0 +1,18 @@ +# Expect three columns, tab separated, as follows: +# - value (Galaxy records this in the Galaxy DB) +# - name (Galaxy shows this in the UI) +# - path (folder name containing the Kraken DB) +# +# e.g. +# plants2018<tab>Plant genomes (2018)<tab>/path/to/krakenDB/plants_2018 +# +# For backward compatibility the Kraken wrapper also accepts: +# - value (Galaxy records this in the Galaxy DB) +# - name (Final part of folder name, Galaxy shows this in the UI) +# - path (Parent folder name, where $path/$name contains the Kraken DB) +# +# e.g. +# plants2018<tab>plants_2018<tab>/path/to/krakenDB +# +# Please avoid this legacy usage, as not all tools using +# the kraken_databases.loc file will understand it.