Mercurial > repos > florianbegusch > qiime2_all
comparison qiime_alignment_mask.xml @ 0:09b7bcb72fa7 draft
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| author | florianbegusch |
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| date | Thu, 24 May 2018 02:11:44 -0400 |
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| -1:000000000000 | 0:09b7bcb72fa7 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="qiime_alignment_mask" name="qiime alignment mask" version="2018.4"> | |
| 3 <description> - Positional conservation and gap filtering.</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2018.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command><![CDATA[ | |
| 8 | |
| 9 qiime alignment mask --i-alignment=$ialignment | |
| 10 | |
| 11 #if str($cmdconfig) != 'None': | |
| 12 --cmd-config=$cmdconfig | |
| 13 #end if | |
| 14 | |
| 15 --o-masked-alignment=omaskedalignment | |
| 16 | |
| 17 #if $pminconservation: | |
| 18 --p-min-conservation=$pminconservation | |
| 19 #end if | |
| 20 | |
| 21 #if $pmaxgapfrequency: | |
| 22 --p-max-gap-frequency=$pmaxgapfrequency | |
| 23 #end if | |
| 24 ; | |
| 25 cp omaskedalignment.qza $omaskedalignment | |
| 26 | |
| 27 ]]></command> | |
| 28 <inputs> | |
| 29 <param format="qza,no_unzip.zip" label="--i-alignment: FeatureData[AlignedSequence] - The alignment to be masked. [required]" name="ialignment" optional="False" type="data"/> | |
| 30 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/> | |
| 31 <param label="--p-min-conservation: The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" name="pminconservation" optional="True" type="float" value="0.4"/> | |
| 32 <param label="--p-max-gap-frequency: The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" name="pmaxgapfrequency" optional="True" type="float" value="1.0"/> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment"/> | |
| 36 </outputs> | |
| 37 <help><![CDATA[ | |
| 38 | |
| 39 Positional conservation and gap filtering. | |
| 40 ------------------------------------------ | |
| 41 | |
| 42 Mask (i.e., filter) unconserved and highly gapped columns from an | |
| 43 alignment. | |
| 44 | |
| 45 Parameters | |
| 46 ---------- | |
| 47 alignment : FeatureData[AlignedSequence] | |
| 48 The alignment to be masked. | |
| 49 max_gap_frequency : Float, optional | |
| 50 The maximum relative frequency of gap characters in a column for the | |
| 51 column to be retained. This relative frequency must be a number between | |
| 52 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without | |
| 53 gap characters, and 1.0 retains all columns regardless of gap character | |
| 54 frequency. | |
| 55 min_conservation : Float, optional | |
| 56 The minimum relative frequency of at least one non-gap character in a | |
| 57 column for that column to be retained. This relative frequency must be | |
| 58 a number between 0.0 and 1.0 (inclusive). For example, if a value of | |
| 59 0.4 is provided, a column will only be retained if it contains at least | |
| 60 one character that is present in at least 40% of the sequences. | |
| 61 | |
| 62 Returns | |
| 63 ------- | |
| 64 masked_alignment : FeatureData[AlignedSequence] | |
| 65 The masked alignment. | |
| 66 ]]> | |
| 67 </help> | |
| 68 </tool> |