Mercurial > repos > iuc > picrust_categorize

annotate categorize_by_function.xml @ 0:a94f4d96045c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
author iuc
date Thu, 08 Dec 2016 06:27:47 -0500
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a94f4d96045c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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1 <tool id="picrust_categorize" name="Categorize by function" version="@WRAPPER_VERSION@.0">
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2 <description>collapse hierarchical data to a specified level</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 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 categorize_by_function.py
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10 -i '$input_fp'
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11 -c $metadata_category
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12 -l $level
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13 -o tempbiom
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14 $format_tab_delimited
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15
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16 @OUTPUT_CONVERSION_COMMANDS@
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17 ]]></command>
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18 <inputs>
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19 <param argument="--input_fp" format="tabular,biom1" type="data" label="Input file" help="the output from the PICRISt predict tool"/>
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20 <param argument="--metadata_category" type="select" multiple="false" label="Metadata category that describes the hierarchy" help="">
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21 <option value="KEGG_Pathways" selected="true">KEGG Pathways</option>
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22 <option value="COG_Category">COG Category</option>
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23 <option value="taxonomy">Using taxonomy metadata</option>
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24 </param>
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25 <param argument="--level" type="integer" value="3" min="1" label="Hierarchy Level"
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26 help="a value of 1 is the highest level, and any higher value nears the leaves of the hierarchy. For instance, if the hierarchy contains 4 levels, specifying 3 would collapse at one level above being fully specified"/>
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27 <param argument="--format_tab_delimited" type="boolean" truevalue="-f" falsevalue="" checked="false" label="output the predicted metagenome table in tab-delimited" help="will contain the metadata lost in the classic output"/>
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28 <expand macro="biom_format_select"/>
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29 </inputs>
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30 <outputs>
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31 <expand macro="biom_output"/>
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32 <data name="out_tabdel" format="tabular" from_work_dir="tempbiom" label="${tool.name} on ${on_string}: metagenome table">
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33 <filter>format_tab_delimited</filter>
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34 </data>
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35 </outputs>
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36 <tests>
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37 <test> <!-- test with Kegg Pathways and json output -->
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38 <param name="input_fp" value="predicted_metagenomes.L3.biom"/>
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39 <param name="metadata_category" value="KEGG_Pathways"/>
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40 <param name="level" value="2"/>
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41 <param name="format_tab_delimited" value="-f"/>
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42 <param name="output_type" value="json"/>
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43 <output name="out_biom" ftype="json">
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44 <assert_contents>
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45 <has_text text="Biological Observation Matrix"/>
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46 <has_text text="generated_by"/>
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47 <has_text text="KEGG_Pathways"/>
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48 <has_text text="Cancers"/>
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49 <not_has_text text="ABC transporters"/>
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50 </assert_contents>
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51 </output>
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52 <output name="out_tabdel" ftype="tabular" file="tempout.table"/>
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53 </test>
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54 <test> <!-- test with COG categories and classic output -->
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55 <param name="input_fp" value="cog_predicted_metagenomes.L2.biom"/>
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56 <param name="metadata_category" value="COG_Category"/>
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57 <param name="level" value="1"/>
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58 <param name="format_tab_delimited" value="-f"/>
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59 <param name="output_type" value="tsv"/>
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60 <output name="out_biom" ftype="tabular" md5="7682875d365f884b399ffa521952dbd8"/>
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61 <output name="out_tabdel" ftype="tabular" md5="e3545484ff53bf8650725573af2ebbb9"/>
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62 </test>
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63 <test> <!-- test with taxonomy metadata and hdf5 output -->
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64 <param name="input_fp" value="observation_table.biom"/>
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65 <param name="metadata_category" value="taxonomy"/>
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66 <param name="level" value="1"/>
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67 <param name="output_type" value="hdf5"/>
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68 <output name="out_biom" ftype="hdf5" file="categorize_biom.hdf5" compare="sim_size"/>
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69 </test>
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70 </tests>
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71 <help>
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72 <![CDATA[
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73 @PICRUST_OVERVIEW@
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74
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75 **Command Documentation**
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76
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77 This module collapses hierarchical data to a specified level for PICRUSt predictions. For instance, often it is useful to examine KEGG results from a higher level within the pathway hierarchy.
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78 Many genes are sometimes involved in multiple pathways, and in these circumstances (also know as a one-to-many relationship), the gene is counted for each pathway.
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79
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80 **Input file:** Output file from the predict tool
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81
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82 ]]>
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83 </help>
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84 <expand macro="citations"/>
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85 </tool>