Mercurial > repos > iuc > picrust_compare_biom
diff macros.xml @ 0:43244ad9e7ef draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 95e0878f4cbd9caadffae7b9bcff4c1795f4c739
author | iuc |
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date | Sat, 20 Jan 2018 03:31:34 -0500 |
parents | |
children | 9168545e09df |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Jan 20 03:31:34 2018 -0500 @@ -0,0 +1,97 @@ +<macros> + <token name="@WRAPPER_VERSION@">1.1.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.1.1">picrust</requirement> + </requirements> + </xml> + + <xml name="version_command"> + <version_command>predict_metagenomes.py --version | cut -d" " -f3 </version_command> + </xml> + + <xml name="otu-reference-precalculated"> + <!-- selection of "gg" picrust parameter reference data file --> + <conditional name="gg"> + <param name="source" type="select" label="Select precalculated file from" help=""> + <option value="ref">Cached Reference</option> + <option value="hist">History</option> + </param> + <when value="ref"> + <param name="precalc" type="select" label="Precalculated input marker gene copy number predictions on per-otu basis"> + <options from_data_table="picrust_precalculated"/> + </param> + </when> + <when value="hist"> + <param name="precalc" type="data" format="tabular" label="Precalculated input marker gene copy number predictions on per-otu basis" + help="files may be downloaded from PICRUSt website (see tool help below)" /> + </when> + </conditional> + </xml> + + <xml name="biom_format_select"> + <param name="output_type" type="select" label="Format of the output BIOM file"> + <option value="hdf5" selected="true">HDF5</option> + <option value="json">JSON</option> + <option value="tsv">Classic (tab-separated text)</option> + </param> + </xml> + + <xml name="biom_format_select_no_json"> + <param name="output_type" type="select" label="Format of the output BIOM file"> + <option value="hdf5" selected="true">HDF5</option> + <option value="tsv">Classic (tab-separated text)</option> + </param> + </xml> + + <xml name="biom_output"> + <data name="out_biom" format="tabular" label="${tool.name} on ${on_string}: Normalized OTUs"> + <change_format> + <when input="output_type" value="json" format="biom1"/> + <when input="output_type" value="tsv" format="tabular"/> + <when input="output_type" value="hdf5" format="h5"/> + </change_format> + </data> + </xml> + + <token name="@OUTPUT_CONVERSION_COMMANDS@"><![CDATA[ + #if $output_type == "hdf5": + && mv tempbiom '$out_biom' + #elif $output_type == "tsv": + && biom convert -i tempbiom -o '$out_biom' --to-tsv + #else: + && biom convert -i tempbiom -o '$out_biom' --to-json + #end if + ]]></token> + + <token name="@PICRUST_OVERVIEW@"> +<![CDATA[ +**PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States** + +The PICRUSt project aims to support prediction of the unobserved character states in a community of +organisms from phylogenetic information about the organisms in that community. The primary application +is to predict gene family abundance (e.g. the metagenome) in environmental DNA samples for which only +marker gene (e.g. 16S rRNA gene) data are available. This is an open source, international, collaborative +bioinformatics project developed in the Huttenhower, Beiko, Langille, Vega Thurber, Knight and Caporaso labs. + +For more information please visit: + +- PICRUSt Documentation: https://picrust.github.io/picrust/ +- PICRUSt GitHub: http://picrust.github.com/ +- PICRUSt Support: https://groups.google.com/d/forum/picrust-users + +**Reference Data** + +Precalculated files: http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/ + +]]> + </token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nbt.2676</citation> + <yield/> + </citations> + </xml> + +</macros>