Mercurial > repos > iuc > humann_associate

annotate humann_associate.xml @ 4:593e19128c58 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 0a3abeca0535457ddf39c394001d61cd2e45afdd
author iuc
date Mon, 24 Apr 2023 18:56:07 +0000
parents 5ae955d5bd2b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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10fdefbf5920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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1 <tool id="humann_associate" name="Perform metadata association" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>on HUMAnN generated table</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="edam_ontology"/>
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7 <expand macro="requirements"/>
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8 <expand macro="version"/>
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9 <command detect_errors="exit_code"><![CDATA[
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10 humann_associate
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11 --input '$input'
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12 --focal-metadatum '$focal_metadatum'
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13 --last-metadatum '$last_metadatum'
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14 --focal-type '$focal_type'
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15 --fdr $fdr
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16 --output '$output'
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17 ]]></command>
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18 <inputs>
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19 <param argument="--input" type="data" format="tsv,tabular" label="Gene family or pathway table with metadata rows at the top"/>
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20 <param argument="--focal-metadatum" type="text" value="" label="Metadatum to test vs. community feature totals">
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21 <sanitizer invalid_char="">
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22 <valid initial="string.ascii_letters,string.digits">
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23 <add value="_" />
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24 </valid>
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25 </sanitizer>
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26 <validator type="empty_field" />
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27 </param>
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28 <param argument="--last-metadatum" type="text" value="" label="End of metadata rows">
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29 <sanitizer invalid_char="">
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30 <valid initial="string.ascii_letters,string.digits">
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31 <add value="_" />
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32 </valid>
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33 </sanitizer>
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34 <validator type="empty_field" />
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35 </param>
2
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36 <param argument="--focal-type" type="select" label="Metadatum type">
0
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37 <option value="continuous">Continuous</option>
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38 <option value="categorical">Categorical</option>
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39 </param>
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40 <param argument="--fdr" type="float" value="0.2" label="FDR threshold"/>
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41 </inputs>
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42 <outputs>
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43 <data format="tabular" name="output"/>
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44 </outputs>
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45 <tests>
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46 <test expect_num_outputs="1">
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47 <param name="input" value="hmp_pathabund.txt"/>
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48 <param name="focal_metadatum" value="STSite"/>
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49 <param name="last_metadatum" value="STSite"/>
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50 <param name="focal_type" value="categorical"/>
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51 <param name="fdr" value="0.2"/>
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52 <output name="output" ftype="tabular">
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53 <assert_contents>
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54 <has_text text="Feature"/>
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55 <has_text text="BRANCHED-CHAIN-AA-SYN-PWY: superpathway of branched amino acid biosynthesis"/>
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56 <has_text text="Level means (|ed)"/>
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57 <has_text text="P-value"/>
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58 <has_text text="Q-value"/>
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59 <has_n_columns n="4"/>
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60 </assert_contents>
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61 </output>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 @HELP_HEADER@
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66
10fdefbf5920 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
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67 When associating metadata with HUMAnN features, it is often beneficial to associate with community totals and avoid testing each
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68 individual feature stratification (to improve statistical power).
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69
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70 This is the approach used by this tool, which can compare feature totals across samples with
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71 1) a single continuous metadatum (via the Spearman Correlation) or
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72 2) a single categorical metadatum (via the Kruskal-Wallis H-test).
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73
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74 Notably, this is a naive approach to association, but it is useful for tutorial purposes.
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75 ]]></help>
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76 <expand macro="citations"/>
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77 </tool>