Mercurial > repos > iuc > biom_convert
diff biom_convert.xml @ 0:501c21cce614 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit 01bf97e10e5491ec878cca24495d8125449dfc1e
| author | iuc |
|---|---|
| date | Tue, 07 Jun 2016 17:26:00 -0400 |
| parents | |
| children | 0de92f0b96ef |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/biom_convert.xml Tue Jun 07 17:26:00 2016 -0400 @@ -0,0 +1,182 @@ +<tool id="biom_convert" name="Convert BIOM" version="@VERSION@.0"> + <description>formats</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> + <expand macro="version_command" /> + <command> + <![CDATA[ + biom convert -i "${input_type.input_table}" -o "${output_table}" + #if str( $input_type.input_type_selector ) == "tsv": + #if $input_type.process_obs_metadata: + --process-obs-metadata "${input_type.process_obs_metadata}" + #end if + #end if + + #if str( $output_type.output_type_selector ) == "tsv": + --to-tsv + #if $output_type.header_key: + --header-key "${output_type.header_key}" + #if $output_type.output_metadata_id: + --output-metadata-id "${output_type.output_metadata_id}" + #end if + --tsv-metadata-formatter "${output_type.tsv_metadata_formatter}" + #end if + #else: + --table-type "${output_type.table_type}" + #if str( $output_type.biom_type.biom_type_selector ) == 'hdf5': + --to-hdf5 + ${output_type.biom_type.collapsed_samples} + ${output_type.biom_type.collapsed_observations} + #else: + --to-json + #end if + #if $output_type.sample_metadata_fp: + --sample-metadata-fp "${output_type.sample_metadata_fp}" + #end if + #if $output_type.observation_metadata_fp: + --observation-metadata-fp "${output_type.observation_metadata_fp}" + #end if + #end if + ]]> + </command> + <inputs> + <conditional name="input_type"> + <param name="input_type_selector" type="select" label="Choose the source BIOM format"> + <option value="tsv" selected="True">Tabular File</option> + <option value="biom">BIOM File</option> + </param> + <when value="tsv"> + <param name="input_table" type="data" format="tabular" label="Tabular File" argument="--input-fp"/> + <param name="process_obs_metadata" type="select" label="Process metadata associated with observations when converting" argument="--process-obs-metadata"> + <option value="" selected="True">Do Not process metadata</option> + <option value="taxonomy">taxonomy</option> + <option value="naive">naive</option> + <option value="sc_separated">sc_separated</option> + </param> + </when> + <when value="biom"> + <param name="input_table" type="data" format="biom1" label="Tabular File" argument="--input-fp"/> + </when> + </conditional> + <conditional name="output_type"> + <param name="output_type_selector" type="select" label="Choose the output type" argument="--to-tsv"> + <option value="tsv">TSV-formatted (classic) table</option> + <option value="biom" selected="True">BIOM</option> + </param> + <when value="tsv"> + <param name="header_key" type="text" value="" label="observation metadata to include" help="Leave empty to ignore" argument="--header-key"/> + <param name="output_metadata_id" type="text" value="" label="name to be given to the observation metadata column" help="Leave empty to ignore" argument="--output-metadata-id"/> + <param name="tsv_metadata_formatter" type="select" label="Method for formatting the observation metadata" argumet="--tsv-metadata-formatter"> + <option value="naive" selected="True">naive</option> + <option value="sc_separated">Semi-colon separated</option> + </param> + </when> + <when value="biom"> + <param name="table_type" type="select" label="Table Type" argument="--table-type"> + <option value="OTU table">OTU table</option> + <option value="Pathway table">Pathway table</option> + <option value="Function table">Function table</option> + <option value="Ortholog table">Ortholog table</option> + <option value="Gene table">Gene table</option> + <option value="Metabolite table">Metabolite table</option> + <option value="Taxon table">Taxon table</option> + <option value="Table" selected="True">Table</option> + </param> + <conditional name="biom_type"> + <param name="biom_type_selector" type="select" label="BIOM format type" argument="--to-json / --to-hdf5"> + <option value="json" selected="True">JSON-formatted table (BIOM1)</option> + <option value="hdf5">HDF5-formatted table (BIOM2)</option> + </param> + <when value="json"> + </when> + <when value="hdf5"> + <param name="collapsed_samples" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed samples" argument="--collapsed-observations"/> + <param name="collapsed_observations" type="boolean" truevalue="" falsevalue="--collapsed-samples" checked="False" label="Use collapsed observations"/> + </when> + </conditional> + <param name="sample_metadata_fp" type="data" format="tabular" optional="True" label="Add sample metadata from metadata mapping file" argument="--sample-metadata-fp"/> + <param name="observation_metadata_fp" type="data" format="tabular" optional="True" label="Add observation metadata from mapping file" argument="--observation-metadata-fp"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="biom1" name="output_table"> + <change_format> + <when input="output_type.output_type_selector" value="tsv" format="tabular" /> + <when input="output_type.biom_type" value="hdf5" format="biom2" /> + </change_format> + </data> + </outputs> + <tests> + <test> + <conditional name="input_type"> + <param name="input_type_selector" value="tsv"/> + <param name="input_table" value="input_abundance_taxonomy_1.tabular" ftype="tabular"/> + <param name="process_obs_metadata" value="taxonomy"/> + </conditional> + <conditional name="output_type"> + <param name="output_type_selector" value="biom"/> + <param name="table_type" value="OTU table"/> + <conditional name="biom_type"> + <param name="biom_type_selector" value="json"/> + </conditional> + <param name="sample_metadata_fp"/> + <param name="observation_metadata_fp"/> + </conditional> + <output name="output_table" file="output_taxonomy_1.biom1.re" ftype="biom1" compare="re_match"/> + </test> + <test> + <conditional name="input_type"> + <param name="input_type_selector" value="tsv"/> + <param name="input_table" value="input_abundance_1.tabular" ftype="tabular"/> + <param name="process_obs_metadata" value=""/> + </conditional> + <conditional name="output_type"> + <param name="output_type_selector" value="biom"/> + <param name="table_type" value="OTU table"/> + <conditional name="biom_type"> + <param name="biom_type_selector" value="json"/> + </conditional> + <param name="sample_metadata_fp"/> + <param name="observation_metadata_fp"/> + </conditional> + <output name="output_table" file="output_1.biom1.re" ftype="biom1" compare="re_match"/> + </test> + </tests> + <help><![CDATA[ + +Usage: biom convert [OPTIONS]:: + + Convert to/from the BIOM table format. + + Convert between BIOM table formats. See examples here: http://biom-format.org/documentation/biom_conversion.html + + Example usage: + + Convert a "classic" BIOM file (tab-separated text) to an HDF5 BIOM formatted OTU table: + + $ biom convert -i table.txt -o table.biom --to-hdf5 + + +Options: + -i, --input-fp PATH The input BIOM table [required] + -o, --output-fp PATH The output BIOM table [required] + -m, --sample-metadata-fp PATH The sample metadata mapping file (will add sample metadata to the input BIOM table, if provided). + --observation-metadata-fp PATH The observation metadata mapping file (will add observation metadata to the input BIOM table, if provided). + --to-json Output as JSON-formatted table. + --to-hdf5 Output as HDF5-formatted table. + --to-tsv Output as TSV-formatted (classic) table. table is a BIOM table with collapsed samples, this will update the sample metadata of the table to the supported HDF5 collapsed format. + --collapsed-observations If --to_hdf5 is passed and the original table is a BIOM table with collapsed observations, this will update the supported HDF5 collapsed format. + --header-key TEXT The observation metadata to include from the input BIOM table file when creating a tsv table file. By default no observation metadata will be included. + --output-metadata-id TEXT The name to be given to the observation metadata column when creating a tsv table file if the column should be renamed. + --table-type OTU table,Pathway table,Function table,Ortholog table,Gene table,Metabolite table,Taxon table,Table The type of the table. + --process-obs-metadata taxonomy,naive,sc_separated Process metadata associated with observations when converting from a classic table. + --tsv-metadata-formatter naive,sc_separated Method for formatting the observation + --help Show this message and exit. + + ]]></help> + <expand macro="citations" /> +</tool>