Mercurial > repos > iuc > qiime_summarize_taxa

comparison summarize_taxa.xml @ 5:50df54a9ae82 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit 3b54163c4f7daff76fcc589c4a9057bb03904380
author iuc
date Sat, 05 Aug 2017 07:19:08 -0400
parents 2f2e4388bd05
children ed9f71643ebc
comparison
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4:f34064a0d89b 5:50df54a9ae82
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</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>
8 <command detect_errors="aggressive"><![CDATA[ 8 <command detect_errors="aggressive"><![CDATA[
9 summarize_taxa.py 9 summarize_taxa.py
10 -i '$otu_table_fp' 10 -i '$otu_table_fp'
11 -o summarize_taxa 11 -o summarize_taxa
12 -L '$level' 12 -L '$level'
13 #if str($mapping) != 'None': 13 #if str($mapping) != 'None':
14 -m '$mapping' 14 -m '$mapping'
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>
29 <inputs> 29 <inputs>
30 <param argument="--otu_table_fp" type="data" format="tabular,tsv,txt,biom" label="Input OTU table" help="(-i/)"/> 30 <param argument="--otu_table_fp" type="data" format="tabular,tsv,txt,biom" label="Input OTU table"/>
31 <param argument="--level" type="select" label="Taxonomic level to summarize by" multiple="True" display="checkboxes"> 31 <param argument="--level" type="select" label="Taxonomic level to summarize by" multiple="true" display="checkboxes">
32 <option value="1">Kingdom</option> 32 <option value="1">Kingdom</option>
33 <option value="2" selected="true">Phylum</option> 33 <option value="2" selected="true">Phylum</option>
34 <option value="3" selected="true">Class</option> 34 <option value="3" selected="true">Class</option>
35 <option value="4" selected="true">Order</option> 35 <option value="4" selected="true">Order</option>
36 <option value="5" selected="true">Family</option> 36 <option value="5" selected="true">Family</option>
37 <option value="6" selected="true">Genus</option> 37 <option value="6" selected="true">Genus</option>
38 <option value="7">Species</option> 38 <option value="7">Species</option>
39 </param> 39 </param>
40 <param argument="--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" optional="True"/> 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" label="Include metadata as string?" truevalue="--md_as_string" falsevalue="" checked="False" 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" label="Report absolute abundance?" truevalue="--absolute_abundance" falsevalue="" checked="False" 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" 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" optional="True"/> 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"/>
45 <param argument="--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" optional="True"/> 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"/>
46 <param argument="--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"/> 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" 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"/> 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" 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"/> 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>
51 <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt" label="${tool.name} on ${on_string}: L1 tab"> 51 <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt" label="${tool.name} on ${on_string}: L1 tab">
52 <filter>"1" in level and suppress_classic_table_output is False</filter> 52 <filter>"1" in level and suppress_classic_table_output is false</filter>
53 </data> 53 </data>
54 <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt" label="${tool.name} on ${on_string}: L2 tab"> 54 <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt" label="${tool.name} on ${on_string}: L2 tab">
55 <filter>"2" in level and suppress_classic_table_output is False</filter> 55 <filter>"2" in level and suppress_classic_table_output is false</filter>
56 </data> 56 </data>
57 <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt" label="${tool.name} on ${on_string}: L3 tab"> 57 <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt" label="${tool.name} on ${on_string}: L3 tab">
58 <filter>"3" in level and suppress_classic_table_output is False</filter> 58 <filter>"3" in level and suppress_classic_table_output is false</filter>
59 </data> 59 </data>
60 <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt" label="${tool.name} on ${on_string}: L4 tab"> 60 <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt" label="${tool.name} on ${on_string}: L4 tab">
61 <filter>"4" in level and suppress_classic_table_output is False</filter> 61 <filter>"4" in level and suppress_classic_table_output is false</filter>
62 </data> 62 </data>
63 <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt" label="${tool.name} on ${on_string}: L5 tab"> 63 <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt" label="${tool.name} on ${on_string}: L5 tab">
64 <filter>"5" in level and suppress_classic_table_output is False</filter> 64 <filter>"5" in level and suppress_classic_table_output is false</filter>
65 </data> 65 </data>
66 <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt" label="${tool.name} on ${on_string}: L6 tab"> 66 <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt" label="${tool.name} on ${on_string}: L6 tab">
67 <filter>"6" in level and suppress_classic_table_output is False</filter> 67 <filter>"6" in level and suppress_classic_table_output is false</filter>
68 </data> 68 </data>
69 <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt" label="${tool.name} on ${on_string}: L7 tab"> 69 <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt" label="${tool.name} on ${on_string}: L7 tab">
70 <filter>"7" in level and suppress_classic_table_output is False</filter> 70 <filter>"7" in level and suppress_classic_table_output is false</filter>
71 </data> 71 </data>
72 </outputs> 72 </outputs>
73 <tests> 73 <tests>
74 <test> 74 <test>
75 <param name="otu_table_fp" value="summarize_taxa/otu_table.biom"/> 75 <param name="otu_table_fp" value="summarize_taxa/otu_table.biom"/>