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1 <?xml version="1.0" ?>
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2 <tool id="qiime_alignment_mask" name="qiime alignment mask"
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3 version="2020.8">
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4 <description>Positional conservation and gap filtering.</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 alignment mask
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10
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11 --i-alignment=$ialignment
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12
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13 --p-max-gap-frequency=$pmaxgapfrequency
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14
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15 --p-min-conservation=$pminconservation
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16
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17 --o-masked-alignment=omaskedalignment
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18
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19 #if str($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 omaskedalignment.qza $omaskedalignment
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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-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked. [required]" name="ialignment" optional="False" type="data" />
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29 <param exclude_max="False" label="--p-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" max="1" min="0" name="pmaxgapfrequency" optional="True" type="float" value="1.0" />
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30 <param exclude_max="False" label="--p-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" max="1" min="0" name="pminconservation" optional="True" type="float" value="0.4" />
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31 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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32
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33 </inputs>
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34
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35 <outputs>
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36 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" />
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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 Positional conservation and gap filtering.
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42 ###############################################################
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43
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44 Mask (i.e., filter) unconserved and highly gapped columns from an
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45 alignment. Default min_conservation was chosen to reproduce the mask
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46 presented in Lane (1991).
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47
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48 Parameters
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49 ----------
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50 alignment : FeatureData[AlignedSequence]
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51 The alignment to be masked.
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52 max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
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53 The maximum relative frequency of gap characters in a column for the
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54 column to be retained. This relative frequency must be a number between
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55 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
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56 gap characters, and 1.0 retains all columns regardless of gap character
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57 frequency.
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58 min_conservation : Float % Range(0, 1, inclusive_end=True), optional
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59 The minimum relative frequency of at least one non-gap character in a
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60 column for that column to be retained. This relative frequency must be
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61 a number between 0.0 and 1.0 (inclusive). For example, if a value of
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62 0.4 is provided, a column will only be retained if it contains at least
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63 one character that is present in at least 40% of the sequences.
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64
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65 Returns
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66 -------
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67 masked_alignment : FeatureData[AlignedSequence]
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68 The masked alignment.
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69 ]]></help>
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70 <macros>
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71 <import>qiime_citation.xml</import>
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72 </macros>
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73 <expand macro="qiime_citation"/>
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74 </tool> |
