Mercurial > repos > bebatut > qiime
view summarize_taxa.xml @ 0:c1bd0c560018 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author | bebatut |
---|---|
date | Tue, 02 Feb 2016 05:50:37 -0500 |
parents | |
children |
line wrap: on
line source
<tool id="qiime_summarize_taxa" name="Summarize taxa" version="1.9.1"> <description>and store results in a new table or appended to an existing mapping file </description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <version_command><![CDATA[ summarize_taxa.py --version ]]> </version_command> <command> <![CDATA[ summarize_taxa.py -i $otu_table_fp -o summarize_taxa -L $level #if str($mapping) != 'None': -m $mapping #end if --md_identifier $md_identifier $md_as_string $absolute_abundance #if str( $lower_percentage ) -l $lower_percentage #end if #if str( $upper_percentage) -u $upper_percentage #end if $transposed_output $suppress_classic_table_output $suppress_biom_table_output ]]> </command> <inputs> <param name="otu_table_fp" type="data" format="tabular,tsv,txt,biom" label="Input OTU table" help="(-i/--otu_table_fp)"/> <param name="level" type="select" label="Taxonomic level to summarize by" help="(-L/--level)" multiple="True" display="checkboxes"> <option value="1" >Kingdom</option> <option value="2" selected="true">Phylum</option> <option value="3" selected="true">Class</option> <option value="4" selected="true">Order</option> <option value="5" selected="true">Family</option> <option value="6" selected="true">Genus</option> <option value="7" >Species</option> </param> <param name="mapping" type="data" format="tabular,tsv,csv" label="Input metadata mapping (optional)" help="If supplied, then the taxon information will be added to this file. This option is useful for coloring PCoA plots by taxon abundance or to perform statistical tests of taxon/mapping associations (-m/--mapping)" optional="True"/> <param name="md_identifier" type="text" value="taxonomy" label="Relevant observation metadata key" help="(--md_identifier)" /> <param name="md_as_string" type="boolean" label="Include metadata as string?" truevalue="--md_as_string" falsevalue="" checked="False" help="By default, metadata is included as list (--md_as_string)" /> <param name="absolute_abundance" type="boolean" label="Report absolute abundance?" truevalue="--absolute_abundance" falsevalue="" checked="False" help="By default, relative abundance is reported (--absolute_abundance)" /> <param name="lower_percentage" type="float" label="Percentage threshold to remove highly present OTU (optional)" help="If present, OTUs having higher absolute abundance are trimmed. To remove OTUs that make up more than 5% of the total dataset you would pass 0.05 (-l/--lower_percentage)" optional="True"/> <param name="upper_percentage" type="float" label="Percentage threshold to remove lowly present OTU (optional)" help="If present, OTUs having lower absolute abundance are trimmed. To remove the OTUs that makes up less than 45% of the total dataset you would pass 0.45 (-u/--upper_percentage)" optional="True"/> <param name="transposed_output" type="boolean" label="Transpose output?" truevalue="--transposed_output" falsevalue="" checked="False" help="If checked, the output will be written transposed from the regular output. This is helpful in cases when you want to use Site Painter to visualize your data (-t/--transposed_output)" /> <param name="suppress_classic_table_output" type="boolean" label="Suppress creation of the classic (TSV) format taxon table?" truevalue="--suppress_classic_table_output" falsevalue="" checked="False" help="This option is ignored if a mapping file is present (--suppress_classic_table_output)" /> <param name="suppress_biom_table_output" type="boolean" label="Suppress creation of the BIOM-formatted taxon table?" truevalue="--suppress_biom_table_output" falsevalue="" checked="False" help="This option is ignored if a mapping file is present (--suppress_biom_table_output)" /> </inputs> <outputs> <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt" label="${tool.name} on ${on_string}: L1 tab"> <filter>"1" in level and suppress_classic_table_output is False</filter> </data> <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt" label="${tool.name} on ${on_string}: L2 tab"> <filter>"2" in level and suppress_classic_table_output is False</filter> </data> <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt" label="${tool.name} on ${on_string}: L3 tab"> <filter>"3" in level and suppress_classic_table_output is False</filter> </data> <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt" label="${tool.name} on ${on_string}: L4 tab"> <filter>"4" in level and suppress_classic_table_output is False</filter> </data> <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt" label="${tool.name} on ${on_string}: L5 tab"> <filter>"5" in level and suppress_classic_table_output is False</filter> </data> <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt" label="${tool.name} on ${on_string}: L6 tab"> <filter>"6" in level and suppress_classic_table_output is False</filter> </data> <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt" label="${tool.name} on ${on_string}: L7 tab"> <filter>"7" in level and suppress_classic_table_output is False</filter> </data> </outputs> <tests> <test> <param name="otu_table_fp" value="pick_open_reference_otus_otu_table_with_taxo.biom"/> <param name="level" value="2,3,4,5,6" /> <param name="mapping" value="validate_mapping_file_corrected_map.tabular"/> <param name="md_identifier" value="taxonomy"/> <param name="md_as_string" value=""/> <param name="delimiter" value=";" /> <param name="absolute_abundance" value=""/> <param name="transposed_output" value=""/> <param name="suppress_classic_table_output" value="" /> <param name="suppress_biom_table_output" value="" /> <output name="L2_tab" value="summarize_taxa_L2.tabular" /> <output name="L3_tab" value="summarize_taxa_L3.tabular" /> <output name="L4_tab" value="summarize_taxa_L4.tabular" /> <output name="L5_tab" value="summarize_taxa_L5.tabular" /> <output name="L6_tab" value="summarize_taxa_L6.tabular" /> </test> </tests> <help><![CDATA[ **What it does** This tool provides summary information of the representation of taxonomic groups within each sample. It takes an OTU table that contains taxonomic information as input. More information about this tool is available on `QIIME documentation <http://qiime.org/scripts/summarize_taxa.html>`_. ]]> </help> <citations> <expand macro="citations" /> </citations> </tool>