Mercurial > repos > iuc > qiime_summarize_taxa

comparison summarize_taxa.xml @ 6:ed9f71643ebc draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 34eaca6eb9d3421c5825a04583779154c30bb324
author iuc
date Sat, 05 Aug 2017 07:59:24 -0400
parents 50df54a9ae82
children 65b11616e81d
comparison
equal deleted inserted replaced
5:50df54a9ae82 6:ed9f71643ebc
1 <tool id="qiime_summarize_taxa" name="Summarize taxa" version="@WRAPPER_VERSION@.0"> 1 <tool id="qiime_summarize_taxa" name="Summarize taxa" version="@WRAPPER_VERSION@.0">
2 <description> and store results in a new table or appended to an existing mapping file (summarize_taxa)</description> 2 <description>and store results in a new table or appended to an existing mapping file (summarize_taxa)</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <version_command>summarize_taxa.py --version</version_command> 7 <version_command>summarize_taxa.py --version</version_command>
39 </param> 39 </param>
40 <param argument="--mapping" type="data" format="tabular,tsv,csv" label="Input metadata mapping" optional="true" 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"/> 40 <param argument="--mapping" type="data" format="tabular,tsv,csv" label="Input metadata mapping" optional="true" 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"/>
41 <param argument="--md_identifier" type="text" value="taxonomy" label="Relevant observation metadata key"/> 41 <param argument="--md_identifier" type="text" value="taxonomy" label="Relevant observation metadata key"/>
42 <param argument="--md_as_string" type="boolean" truevalue="--md_as_string" falsevalue="" checked="false" label="Include metadata as string?" help="By default, metadata is included as list"/> 42 <param argument="--md_as_string" type="boolean" truevalue="--md_as_string" falsevalue="" checked="false" label="Include metadata as string?" help="By default, metadata is included as list"/>
43 <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="Report absolute abundance?" help="By default, relative abundance is reported"/> 43 <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="Report absolute abundance?" help="By default, relative abundance is reported"/>
44 <param argument="lower_percentage" type="float" optional="true" label="Percentage threshold to remove highly present OTU" 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"/> 44 <param argument="--lower_percentage" type="float" value="" optional="true" label="Percentage threshold to remove highly present OTU" 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"/>
45 <param argument="--upper_percentage" type="float" label="Percentage threshold to remove lowly present OTU" 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"/> 45 <param argument="--upper_percentage" type="float" value="" label="Percentage threshold to remove lowly present OTU" 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"/>
46 <param argument="--transposed_output" type="boolean" truevalue="--transposed_output" falsevalue="" checked="false" label="Transpose output?" 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"/> 46 <param argument="--transposed_output" type="boolean" truevalue="--transposed_output" falsevalue="" checked="false" label="Transpose output?" 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"/>
47 <param argument="--suppress_classic_table_output" type="boolean" truevalue="--suppress_classic_table_output" falsevalue="" checked="false" label="Suppress creation of the classic (TSV) format taxon table?" help="This option is ignored if a mapping file is present"/> 47 <param argument="--suppress_classic_table_output" type="boolean" truevalue="--suppress_classic_table_output" falsevalue="" checked="false" label="Suppress creation of the classic (TSV) format taxon table?" help="This option is ignored if a mapping file is present"/>
48 <param argument="--suppress_biom_table_output" type="boolean" truevalue="--suppress_biom_table_output" falsevalue="" checked="false" label="Suppress creation of the BIOM-formatted taxon table?" help="This option is ignored if a mapping file is present"/> 48 <param argument="--suppress_biom_table_output" type="boolean" truevalue="--suppress_biom_table_output" falsevalue="" checked="false" label="Suppress creation of the BIOM-formatted taxon table?" help="This option is ignored if a mapping file is present"/>
49 </inputs> 49 </inputs>
50 <outputs> 50 <outputs>