Mercurial > repos > iuc > qiime_summarize_taxa

comparison summarize_taxa.xml @ 7:65b11616e81d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 528ca3b14c2ca9b7ac18a0f9d80a5f4a235707bf
author iuc
date Mon, 16 Oct 2017 05:02:19 -0400
parents ed9f71643ebc
children f123155af742
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6:ed9f71643ebc 7:65b11616e81d
15 #end if 15 #end if
16 --md_identifier $md_identifier 16 --md_identifier $md_identifier
17 $md_as_string 17 $md_as_string
18 $absolute_abundance 18 $absolute_abundance
19 #if str( $lower_percentage ) 19 #if str( $lower_percentage )
20 -l '$lower_percentage' 20 -l $lower_percentage
21 #end if 21 #end if
22 #if str( $upper_percentage) 22 #if str( $upper_percentage)
23 -u '$upper_percentage' 23 -u $upper_percentage
24 #end if 24 #end if
25 $transposed_output 25 $transposed_output
26 $suppress_classic_table_output 26 $suppress_classic_table_output
27 $suppress_biom_table_output 27 $suppress_biom_table_output
28 ]]></command> 28 ]]></command>
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" 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"/> 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" 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"/> 45 <param argument="--upper_percentage" type="float" value="" optional="true" 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>