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1 <?xml version="1.0" ?>
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2 <tool id="qiime_alignment_mask" name="qiime alignment mask" version="2019.4">
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3 <description> - Positional conservation and gap filtering.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime alignment mask
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9
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10 --i-alignment=$ialignment
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11
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12 --o-masked-alignment=omaskedalignment
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13
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14 #if $pmaxgapfrequency:
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15 --p-max-gap-frequency=$pmaxgapfrequency
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16 #end if
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17
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18 #if $pminconservation:
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19 --p-min-conservation=$pminconservation
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20 #end if
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21
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22 cp omaskedalignment.qza $omaskedalignment
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23 ]]></command>
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24 <inputs>
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25 <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked. [required]" name="ialignment" optional="False" type="data"/>
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26 <param label="--p-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" name="pmaxgapfrequency" optional="True" type="float" min="0" max="1" exclude_max="False" value="1.0"/>
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27 <param label="--p-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" name="pminconservation" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.4"/>
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28 </inputs>
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29 <outputs>
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30 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment"/>
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31 </outputs>
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32 <help><![CDATA[
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33 Positional conservation and gap filtering.
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34 ##########################################
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35
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36 Mask (i.e., filter) unconserved and highly gapped columns from an
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37 alignment. Default min_conservation was chosen to reproduce the mask
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38 presented in Lane (1991).
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39
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40 Parameters
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41 ----------
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42 alignment : FeatureData[AlignedSequence]
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43 The alignment to be masked.
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44 max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional
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45 The maximum relative frequency of gap characters in a column for the
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46 column to be retained. This relative frequency must be a number between
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47 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without
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48 gap characters, and 1.0 retains all columns regardless of gap character
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49 frequency.
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50 min_conservation : Float % Range(0, 1, inclusive_end=True), optional
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51 The minimum relative frequency of at least one non-gap character in a
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52 column for that column to be retained. This relative frequency must be
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53 a number between 0.0 and 1.0 (inclusive). For example, if a value of
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54 0.4 is provided, a column will only be retained if it contains at least
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55 one character that is present in at least 40% of the sequences.
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56
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57 Returns
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58 -------
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59 masked_alignment : FeatureData[AlignedSequence]
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60 The masked alignment.
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61 ]]></help>
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62 <macros>
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63 <import>qiime_citation.xml</import>
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64 </macros>
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65 <expand macro="qiime_citation"/>
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66 </tool>
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