Mercurial > repos > iuc > picrust_normalize_by_copy_number
diff normalize_by_copy_number.xml @ 1:76c040c8b9fc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit d2e3207994a1a796366a0026396f40f8b88af0c3
author | iuc |
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date | Wed, 30 Aug 2017 04:49:31 -0400 |
parents | |
children | 2e62e32d4f33 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/normalize_by_copy_number.xml Wed Aug 30 04:49:31 2017 -0400 @@ -0,0 +1,63 @@ +<tool id="picrust_normalize_by_copy_number" name="Normalize" version="@WRAPPER_VERSION@.0"> + <description>the relative abundance of each OTU by the predicted number of 16S copies</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + normalize_by_copy_number.py + -i '$input_data' + -o tempbiom + -c '$gg.precalc' + + @OUTPUT_CONVERSION_COMMANDS@ + ]]></command> + <inputs> + <param name="input_data" type="data" format="biom1,h5" label="Input file" help="biom file"/> + <expand macro="otu-reference-precalculated"/> + <expand macro="biom_format_select"/> + </inputs> + <outputs> + <expand macro="biom_output"/> + </outputs> + <tests> + <test> <!-- test with biom input --> + <param name="input_data" value="closed_picked_otus.biom"/> + <param name="source" value="hist"/> + <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/> + <param name="output_type" value="json"/> + <output name="out_biom" ftype="biom1"> + <assert_contents> + <has_text text="Biological Observation Matrix"/> + <has_text text="generated_by"/> + </assert_contents> + </output> + </test> + <test> <!-- test with QIIME input and classic output --> + <param name="input_data" value="closed_picked_otus.tab"/> + <param name="source" value="hist"/> + <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/> + <param name="output_type" value="tsv"/> + <output name="out_biom" file="normalized_otus.classic" ftype="tabular"/> + </test> + </tests> + <help> +<![CDATA[ +@PICRUST_OVERVIEW@ + +**Command Documenation** + +This module corrects the abundance of each OTU to better reflect the true organism abundance by normalizing by PICRUSt's prediction of 16S copy number for each OTU. + +Please ensure that you have properly created your OTU table to be compatible with PICRUSt by following this guide_. +A sample file can be downloaded here_ + +Make sure that you specify an appropriate 16S database for this command (usually 16S 13_5). + +.. _guide: http://picrust.github.com/picrust/methods/constructing_reference_otus.html +.. _here: https://raw.github.com/picrust/picrust/master/tutorials/hmp_mock_16S.tab +]]> + </help> + <expand macro="citations"/> +</tool>