| Previous changeset 8:72ed72122deb (2023-01-21) Next changeset 10:a4db66553a61 (2023-10-26) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 4d77c1e4bd9f6876ee338858a8cd4c7e9528d54c |
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modified:
biom_convert.xml macros.xml |
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| diff -r 72ed72122deb -r e177a8ea0bf1 biom_convert.xml --- a/biom_convert.xml Sat Jan 21 11:17:10 2023 +0000 +++ b/biom_convert.xml Wed Sep 13 18:53:51 2023 +0000 |
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| @@ -56,8 +56,8 @@ <option value="biom">BIOM File</option> </param> <when value="tsv"> - <param name="input_fp" argument="--input-fp" type="data" format="tabular" label="Input table" /> - <param name="process_obs_metadata" argument="--process-obs-metadata" type="select" label="Process metadata associated with observations when converting"> + <param argument="--input-fp" type="data" format="tabular" label="Input table" /> + <param argument="--process-obs-metadata" type="select" label="Process metadata associated with observations when converting"> <option value="" selected="True">Do Not process metadata</option> <option value="taxonomy">taxonomy</option> <option value="naive">naive</option> @@ -65,7 +65,7 @@ </param> </when> <when value="biom"> - <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="Input BIOM table"/> + <param argument="--input-fp" type="data" format="biom1" label="Input BIOM table"/> </when> </conditional> <conditional name="output"> @@ -74,15 +74,15 @@ <option value="biom" selected="True">BIOM</option> </param> <when value="tsv"> - <param name="header_key" argument="--header-key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" /> - <param name="output_metadata_id" argument="--output-metadata-id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" /> - <param name="tsv_metadata_formatter" argument="--tsv-metadata-formatter" type="select" label="Method for formatting the observation metadata" > + <param argument="--header-key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" /> + <param argument="--output-metadata-id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" /> + <param argument="--tsv-metadata-formatter" type="select" label="Method for formatting the observation metadata" > <option value="naive" selected="True">naive</option> <option value="sc_separated">Semi-colon separated</option> </param> </when> <when value="biom"> - <param name="table_type" argument="--table-type" type="select" label="Table Type" > + <param argument="--table-type" type="select" label="Table Type" > <option value="OTU table">OTU table</option> <option value="Pathway table">Pathway table</option> <option value="Function table">Function table</option> @@ -100,12 +100,12 @@ <when value="json"> </when> <when value="hdf5"> - <param name="collapsed_observations" argument="--collapsed-observations" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed samples"/> - <param name="collapsed_samples" argument="--collapsed-samples" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed observations"/> + <param argument="--collapsed-observations" type="boolean" truevalue="--collapsed-observations" falsevalue="" checked="False" label="Use collapsed observations"/> + <param argument="--collapsed-samples" type="boolean" truevalue="--collapsed-samples" falsevalue="" checked="False" label="Use collapsed samples"/> </when> </conditional> - <param name="sample_metadata_fp" argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" /> - <param name="observation_metadata_fp" argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" /> + <param argument="--sample-metadata-fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" /> + <param argument="--observation-metadata-fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" /> </when> </conditional> </inputs> |
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| diff -r 72ed72122deb -r e177a8ea0bf1 macros.xml --- a/macros.xml Sat Jan 21 11:17:10 2023 +0000 +++ b/macros.xml Wed Sep 13 18:53:51 2023 +0000 |
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| @@ -6,7 +6,7 @@ </requirements> </xml> <token name="@TOOL_VERSION@">2.1.14</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">21.05</token> <xml name="version_command"> <version_command>biom --version</version_command> |