Mercurial > repos > iuc > qiime_summarize_taxa

annotate 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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1 <tool id="qiime_summarize_taxa" name="Summarize taxa" version="@WRAPPER_VERSION@.0">
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2 <description>and store results in a new table or appended to an existing mapping file (summarize_taxa)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <version_command>summarize_taxa.py --version</version_command>
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8 <command detect_errors="aggressive"><![CDATA[
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9 summarize_taxa.py
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10 -i '$otu_table_fp'
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11 -o summarize_taxa
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12 -L '$level'
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13 #if str($mapping) != 'None':
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14 -m '$mapping'
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15 #end if
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16 --md_identifier $md_identifier
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17 $md_as_string
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18 $absolute_abundance
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19 #if str( $lower_percentage )
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20 -l $lower_percentage
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21 #end if
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22 #if str( $upper_percentage)
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23 -u $upper_percentage
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24 #end if
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25 $transposed_output
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26 $suppress_classic_table_output
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27 $suppress_biom_table_output
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28 ]]></command>
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29 <inputs>
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30 <param argument="--otu_table_fp" type="data" format="tabular,tsv,txt,biom" label="Input OTU table"/>
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31 <param argument="--level" type="select" label="Taxonomic level to summarize by" multiple="true" display="checkboxes">
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32 <option value="1">Kingdom</option>
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33 <option value="2" selected="true">Phylum</option>
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34 <option value="3" selected="true">Class</option>
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35 <option value="4" selected="true">Order</option>
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36 <option value="5" selected="true">Family</option>
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37 <option value="6" selected="true">Genus</option>
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38 <option value="7">Species</option>
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39 </param>
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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"/>
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41 <param argument="--md_identifier" type="text" value="taxonomy" label="Relevant observation metadata key"/>
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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"/>
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43 <param argument="--absolute_abundance" type="boolean" truevalue="--absolute_abundance" falsevalue="" checked="false" label="Report absolute abundance?" help="By default, relative abundance is reported"/>
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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"/>
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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"/>
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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"/>
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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"/>
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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"/>
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49 </inputs>
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50 <outputs>
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51 <data name="L1_tab" format="tabular" from_work_dir="summarize_taxa/*_L1.txt" label="${tool.name} on ${on_string}: L1 tab">
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52 <filter>"1" in level and suppress_classic_table_output is false</filter>
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53 </data>
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54 <data name="L2_tab" format="tabular" from_work_dir="summarize_taxa/*_L2.txt" label="${tool.name} on ${on_string}: L2 tab">
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55 <filter>"2" in level and suppress_classic_table_output is false</filter>
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56 </data>
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57 <data name="L3_tab" format="tabular" from_work_dir="summarize_taxa/*_L3.txt" label="${tool.name} on ${on_string}: L3 tab">
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58 <filter>"3" in level and suppress_classic_table_output is false</filter>
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59 </data>
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60 <data name="L4_tab" format="tabular" from_work_dir="summarize_taxa/*_L4.txt" label="${tool.name} on ${on_string}: L4 tab">
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61 <filter>"4" in level and suppress_classic_table_output is false</filter>
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62 </data>
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63 <data name="L5_tab" format="tabular" from_work_dir="summarize_taxa/*_L5.txt" label="${tool.name} on ${on_string}: L5 tab">
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64 <filter>"5" in level and suppress_classic_table_output is false</filter>
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65 </data>
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66 <data name="L6_tab" format="tabular" from_work_dir="summarize_taxa/*_L6.txt" label="${tool.name} on ${on_string}: L6 tab">
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67 <filter>"6" in level and suppress_classic_table_output is false</filter>
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68 </data>
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69 <data name="L7_tab" format="tabular" from_work_dir="summarize_taxa/*_L7.txt" label="${tool.name} on ${on_string}: L7 tab">
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70 <filter>"7" in level and suppress_classic_table_output is false</filter>
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71 </data>
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72 </outputs>
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73 <tests>
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74 <test>
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75 <param name="otu_table_fp" value="summarize_taxa/otu_table.biom"/>
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76 <param name="level" value="2,3,4,5,6"/>
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77 <param name="mapping" value="summarize_taxa/map.txt"/>
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78 <param name="md_identifier" value="taxonomy"/>
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79 <param name="md_as_string" value=""/>
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80 <param name="absolute_abundance" value=""/>
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81 <param name="transposed_output" value=""/>
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82 <param name="suppress_classic_table_output" value=""/>
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83 <param name="suppress_biom_table_output" value=""/>
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84 <output name="L2_tab" value="summarize_taxa/1_L2.txt"/>
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85 <output name="L3_tab" value="summarize_taxa/1_L3.txt"/>
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86 <output name="L4_tab" value="summarize_taxa/1_L4.txt"/>
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87 <output name="L5_tab" value="summarize_taxa/1_L5.txt"/>
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88 <output name="L6_tab" value="summarize_taxa/1_L6.txt"/>
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89 </test>
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90 <test>
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91 <param name="otu_table_fp" value="summarize_taxa/otu_table.biom"/>
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92 <param name="level" value="3,6"/>
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93 <param name="md_identifier" value="taxonomy"/>
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94 <param name="md_as_string" value=""/>
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95 <param name="absolute_abundance" value=""/>
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96 <param name="transposed_output" value=""/>
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97 <param name="suppress_classic_table_output" value=""/>
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98 <param name="suppress_biom_table_output" value=""/>
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99 <output name="L3_tab" value="summarize_taxa/2_L3.txt"/>
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100 <output name="L6_tab" value="summarize_taxa/2_L6.txt"/>
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101 </test>
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102 </tests>
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103 <help><![CDATA[
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104 **What it does**
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105
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106 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.
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107
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108 More information about this tool is available on
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109 `QIIME documentation <http://qiime.org/scripts/summarize_taxa.html>`_.
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110 ]]></help>
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111 <citations>
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112 <expand macro="citations"/>
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113 </citations>
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114 </tool>