Mercurial > repos > iuc > drep_compare
changeset 3:d99788b71ce7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/drep commit 91d5bae878afa54d8264c1ca89c79b2d26ef35ad
| author | iuc |
|---|---|
| date | Wed, 15 Mar 2023 11:04:40 +0000 |
| parents | 54aa421c2911 |
| children | 965f73e77296 |
| files | macros.xml test-data/extra_weight_table_test |
| diffstat | 2 files changed, 24 insertions(+), 1 deletions(-) [+] |
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--- a/macros.xml Mon Jun 27 13:39:55 2022 +0000 +++ b/macros.xml Wed Mar 15 11:04:40 2023 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">3.3.0</token> + <token name="@TOOL_VERSION@">3.4.2</token> <token name="@VERSION_SUFFIX@">0</token> <token name="@PROFILE@">20.01</token> <xml name="biotools"> @@ -271,6 +271,7 @@ <param argument="--N50_weight" type="float" value=".5" label="Weight of log(genome N50)"/> <param argument="--size_weight" type="float" value="0" label="Weight of log(genome size)"/> <param argument="--centrality_weight" type="float" value="1" label="Weight of (centrality - S_ani)"/> + <param argument="--extra_weight_table" type="data" format="tabular" multiple="false" optional="true" label="Genome specific extra weight"/> </section> </xml> <xml name="test_default_scoring_options"> @@ -283,6 +284,17 @@ <param name="centrality_weight" value="1"/> </section> </xml> + <xml name="test_extra_weight_table_scoring_options"> + <section name="scoring"> + <param name="completeness_weight" value="1"/> + <param name="contamination_weight" value="5"/> + <param name="strain_heterogeneity_weight" value="1"/> + <param name="N50_weight" value=".5" /> + <param name="size_weight" value="0"/> + <param name="centrality_weight" value="1"/> + <param name="extra_weight_table" ftype="tabular" value="extra_weight_table_test"/> + </section> + </xml> <token name="@SCORING_OPTIONS@"><![CDATA[ --completeness_weight $scoring.completeness_weight --contamination_weight $scoring.contamination_weight @@ -290,6 +302,10 @@ --N50_weight $scoring.N50_weight --size_weight $scoring.size_weight --centrality_weight $scoring.centrality_weight + #if str($extra_weight_table) != 'None' + --extra_weight_table $extra_weight_table + #end if + ]]></token> <xml name="warning_options"> @@ -483,6 +499,8 @@ weight of log(genome N50) (default: 0.5) -sizeW SIZE_WEIGHT, --size_weight SIZE_WEIGHT weight of log(genome size) (default: 0) + -extraW EXTRA_WEIGHT_TABLE, --extra_weight_table EXTRA_WEIGHT_TABLE + Path to a tab-separated file with two-columns, no headers, listing genome and extra score to apply to that genome (optional) ]]></token>