Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2/qiime_alignment_mask.xml @ 29:3ba9833030c1 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 13:12:49 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2/qiime_alignment_mask.xml Fri Sep 04 13:12:49 2020 +0000 @@ -0,0 +1,74 @@ +<?xml version="1.0" ?> +<tool id="qiime_alignment_mask" name="qiime alignment mask" + version="2020.8"> + <description>Positional conservation and gap filtering.</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime alignment mask + +--i-alignment=$ialignment + +--p-max-gap-frequency=$pmaxgapfrequency + +--p-min-conservation=$pminconservation + +--o-masked-alignment=omaskedalignment + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp omaskedalignment.qza $omaskedalignment + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-alignment: ARTIFACT FeatureData[AlignedSequence] The alignment to be masked. [required]" name="ialignment" optional="False" type="data" /> + <param exclude_max="False" label="--p-max-gap-frequency: PROPORTION Range(0, 1, inclusive_end=True) The maximum relative frequency of gap characters in a column for the column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive), where 0.0 retains only those columns without gap characters, and 1.0 retains all columns regardless of gap character frequency. [default: 1.0]" max="1" min="0" name="pmaxgapfrequency" optional="True" type="float" value="1.0" /> + <param exclude_max="False" label="--p-min-conservation: PROPORTION Range(0, 1, inclusive_end=True) The minimum relative frequency of at least one non-gap character in a column for that column to be retained. This relative frequency must be a number between 0.0 and 1.0 (inclusive). For example, if a value of 0.4 is provided, a column will only be retained if it contains at least one character that is present in at least 40% of the sequences. [default: 0.4]" max="1" min="0" name="pminconservation" optional="True" type="float" value="0.4" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="qza" label="${tool.name} on ${on_string}: maskedalignment.qza" name="omaskedalignment" /> + + </outputs> + + <help><![CDATA[ +Positional conservation and gap filtering. +############################################################### + +Mask (i.e., filter) unconserved and highly gapped columns from an +alignment. Default min_conservation was chosen to reproduce the mask +presented in Lane (1991). + +Parameters +---------- +alignment : FeatureData[AlignedSequence] + The alignment to be masked. +max_gap_frequency : Float % Range(0, 1, inclusive_end=True), optional + 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. +min_conservation : Float % Range(0, 1, inclusive_end=True), optional + 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. + +Returns +------- +masked_alignment : FeatureData[AlignedSequence] + The masked alignment. + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file