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1 <?xml version="1.0" ?>
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2 <tool id="qiime_fragment-insertion_filter-features" name="qiime fragment-insertion filter-features"
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3 version="2020.8">
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4 <description>Filter fragments in tree from table.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime fragment-insertion filter-features
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10
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11 --i-table=$itable
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12
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13 --i-tree=$itree
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14
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15 --o-filtered-table=ofilteredtable
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16
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17 --o-removed-table=oremovedtable
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18
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19 #if str($examples) != 'None':
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20 --examples=$examples
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21 #end if
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22
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23 ;
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24 cp oremovedtable.qza $oremovedtable
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25
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26 ]]></command>
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27 <inputs>
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28 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] A feature-table which needs to filtered down to those fragments that are contained in the tree, e.g. result of a Deblur or DADA2 run. [required]" name="itable" optional="False" type="data" />
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29 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT The tree resulting from inserting fragments into a Phylogeny[Rooted] reference phylogeny, i.e. the output of function \'sepp\' [required]" name="itree" optional="False" type="data" />
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30 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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31
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32 </inputs>
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33
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34 <outputs>
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35 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable" />
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36 <data format="qza" label="${tool.name} on ${on_string}: removedtable.qza" name="oremovedtable" />
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37
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38 </outputs>
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39
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40 <help><![CDATA[
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41 Filter fragments in tree from table.
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42 ###############################################################
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43
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44 Filters fragments not inserted into a phylogenetic tree from a feature-
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45 table. Some fragments computed by e.g. Deblur or DADA2 are too remote to
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46 get inserted by SEPP into a reference phylogeny. To be able to use the
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47 feature-table for downstream analyses like computing Faith's PD or UniFrac,
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48 the feature-table must be cleared of fragments that are not part of the
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49 phylogenetic tree, because their path length can otherwise not be
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50 determined. Typically, the number of rejected fragments is low (<= 10), but
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51 it might be worth to inspect the ratio of reads assigned to those rejected
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52 fragments.
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53
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54 Parameters
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55 ----------
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56 table : FeatureTable[Frequency]
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57 A feature-table which needs to filtered down to those fragments that
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58 are contained in the tree, e.g. result of a Deblur or DADA2 run.
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59 tree : Phylogeny[Rooted]
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60 The tree resulting from inserting fragments into a reference phylogeny,
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61 i.e. the output of function 'sepp'
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62
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63 Returns
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64 -------
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65 filtered_table : FeatureTable[Frequency]
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66 The input table minus those fragments that were not part of the tree.
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67 This feature-table can be used for downstream analyses like
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68 phylogenetic alpha- or beta- diversity computation.
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69 removed_table : FeatureTable[Frequency]
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70 Those fragments that got removed from the input table, because they
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71 were not part of the tree. This table is mainly used for quality
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72 control, e.g. to inspect the ratio of removed reads per sample from the
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73 input table. You can ignore this table for downstream analyses.
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74 ]]></help>
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75 <macros>
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76 <import>qiime_citation.xml</import>
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77 </macros>
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78 <expand macro="qiime_citation"/>
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79 </tool> |
