Mercurial > repos > iuc > picrust_categorize

annotate categorize_by_function.xml @ 4:bee527de98ac draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
author iuc
date Thu, 28 Nov 2019 15:53:32 -0500
parents fd5533e57354
children 36e87158ef04
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1 <tool id="picrust_categorize" name="Categorize" version="@WRAPPER_VERSION@.0">
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2 <description>by collapsing hierarchical data to a specified functional 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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15 @OUTPUT_CONVERSION_COMMANDS@
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16 ]]></command>
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17 <inputs>
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18 <param argument="--input_fp" format="biom1,h5" type="data" label="Input file" help="Biom file that is output from the PICRISt predict tool"/>
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19 <param argument="--metadata_category" type="select" multiple="false" label="Metadata category that describes the hierarchy" help="">
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20 <option value="KEGG_Pathways" selected="true">KEGG Pathways</option>
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21 <option value="COG_Category">COG Category</option>
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22 <option value="taxonomy">Using taxonomy metadata</option>
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23 </param>
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24 <param argument="--level" type="integer" value="3" min="1" label="Hierarchy Level"
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25 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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26 <expand macro="biom_format_select"/>
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27 </inputs>
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28 <outputs>
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29 <expand macro="biom_output"/>
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30 </outputs>
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31 <tests>
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32 <test> <!-- test with Kegg Pathways and json output -->
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33 <param name="input_fp" value="predicted_metagenomes.L3.biom"/>
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34 <param name="metadata_category" value="KEGG_Pathways"/>
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35 <param name="level" value="2"/>
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36 <param name="output_type" value="json"/>
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37 <output name="out_biom" ftype="biom1">
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38 <assert_contents>
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39 <has_text text="Biological Observation Matrix"/>
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40 <has_text text="generated_by"/>
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41 <has_text text="KEGG_Pathways"/>
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42 <has_text text="Cancers"/>
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43 <not_has_text text="ABC transporters"/>
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44 </assert_contents>
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45 </output>
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46 </test>
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47 <test> <!-- test with COG categories and classic output -->
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48 <param name="input_fp" value="cog_predicted_metagenomes.L2.biom"/>
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49 <param name="metadata_category" value="COG_Category"/>
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50 <param name="level" value="1"/>
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51 <param name="output_type" value="tsv"/>
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52 <output name="out_biom" ftype="tabular" md5="7682875d365f884b399ffa521952dbd8"/>
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53 </test>
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54 <test> <!-- test with taxonomy metadata and hdf5 output -->
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55 <param name="input_fp" value="observation_table.biom"/>
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56 <param name="metadata_category" value="taxonomy"/>
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57 <param name="level" value="1"/>
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58 <param name="output_type" value="hdf5"/>
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59 <output name="out_biom" ftype="h5" file="categorize_biom.hdf5" compare="sim_size"/>
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60 </test>
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61 </tests>
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62 <help>
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63 <![CDATA[
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64 @PICRUST_OVERVIEW@
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65
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66 **Command Documentation**
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67
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68 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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69 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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70
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71 **Input file:** Output file from the predict tool
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72
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73 ]]>
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74 </help>
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75 <expand macro="citations"/>
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76 </tool>