Mercurial > repos > iuc > humann_renorm_table

annotate humann_renorm_table.xml @ 0:e3391ccf21a0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
author iuc
date Wed, 12 May 2021 09:05:14 +0000
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1 <tool id="humann_renorm_table" name="Renormalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>a 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_renorm_table
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11 --input '$input'
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12 -o '$output'
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13 --units '$units'
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14 --mode '$mode'
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15 --special '$special'
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16 $update_snames
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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/pathway table"/>
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20 <param argument="--units" type="select" label="Normalization scheme">
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21 <option value="cpm" selected="true">Copies per million</option>
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22 <option value="relab">Relative abundance</option>
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23 </param>
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24 <param argument="--mode" type="select" label="Normalization level">
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25 <option value="community" selected="true">Normalization of all levels by community total</option>
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26 <option value="levelwise">Normalization of all levels by levelwise total</option>
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27 </param>
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28 <param argument="--special" type='boolean' truevalue='y' falsevalue='n' checked="true" label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
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29 <param argument="--update-snames" type='boolean' truevalue='--update-snames' falsevalue='' checked="true" label="Update '-RPK' in sample names to appropriate suffix?"/>
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30 </inputs>
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31 <outputs>
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32 <data format="tabular" name="output"/>
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33 </outputs>
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34 <tests>
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35 <test expect_num_outputs="1">
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36 <param name="input" value="demo_pathabundance.tsv"/>
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37 <param name="units" value="cpm"/>
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38 <param name="mode" value="community"/>
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39 <param name="special" value="n"/>
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40 <param name="update_snames" value=""/>
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41 <output name="output" ftype="tabular" file="cpm_community_renormalized_pathway_abundance.tsv">
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42 <assert_contents>
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43 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis" />
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44 <has_text text="578694" />
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45 </assert_contents>
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46 </output>
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47 </test>
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48 <test expect_num_outputs="1">
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49 <param name="input" value="demo_pathabundance.tsv"/>
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50 <param name="units" value="relab"/>
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51 <param name="mode" value="levelwise"/>
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52 <param name="special" value="y"/>
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53 <param name="update_snames" value=""/>
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54 <output name="output" ftype="tabular" file="relab_levelwise_renormalized_pathway_abundance.tsv">
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55 <assert_contents>
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56 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified" />
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57 <has_text text="0.630281" />
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58 </assert_contents>
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59 </output>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63 @HELP_HEADER@
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64
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65 HUMAnN quantifies genes and pathways in units of RPKs (reads per kilobase). These account for gene length but not sample sequencing depth.
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66 While there are some applications, e.g. strain profiling, where RPK units are superior to depth-normalized units, most of the
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67 time a user will renormalize their samples prior to downstream analysis.
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68
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69 This tool provides the choice to normalize to relative abundance or copies per million (CPM) units. Both of these represent
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70 "total sum scaling (TSS)"-style normalization: in the former case, each sample is constrained to sum to 1, whereas in the
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71 latter case (CPMs) samples are constrained to sum to 1 million. Units out of 1 million are often more convenient for tables
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72 with many, many features (such as genefamilies.tsv tables).
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73
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74 Note: CPM as used here does not refer to unnormalized COUNTS per million, but rather copies per million.
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75 CPMs as used here are a generic analog of the TPM (transcript per million) unit in RNA-seq. You may wish to use the
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76 abbreviation CoPM for added clarity.
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77
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78 By default, this tool normalizes all stratification levels to the sum of all community feature totals, but other options
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79 (such as level-wise normalization) are supported. "Special" features (such as UNMAPPED) can be included or excluded in the
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80 normalization process.
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81 ]]></help>
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82 <expand macro="citations"/>
e3391ccf21a0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
iuc
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83 </tool>