Mercurial > repos > florianbegusch > qiime2_suite
diff qiime2-2020.8/qiime_diversity_mantel.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2-2020.8/qiime_diversity_mantel.xml Fri Sep 04 12:44:24 2020 +0000 @@ -0,0 +1,111 @@ +<?xml version="1.0" ?> +<tool id="qiime_diversity_mantel" name="qiime diversity mantel" + version="2020.8"> + <description>Apply the Mantel test to two distance matrices</description> + <requirements> + <requirement type="package" version="2020.8">qiime2</requirement> + </requirements> + <command><![CDATA[ +qiime diversity mantel + +--i-dm1=$idm1 + +--i-dm2=$idm2 + +#if str($pmethod) != 'None': +--p-method=$pmethod +#end if + +--p-permutations=$ppermutations + +#if $pintersectids: + --p-intersect-ids +#end if + +#if str($plabel1): + --p-label1=$plabel1 +#end if +#if str($plabel2): + --p-label2=$plabel2 +#end if +--o-visualization=ovisualization + +#if str($examples) != 'None': +--examples=$examples +#end if + +; +cp ofiltereddistancematrix.qza $ofiltereddistancematrix + +; +qiime tools export ovisualization.qzv --output-path out +&& mkdir -p '$ovisualization.files_path' +&& cp -r out/* '$ovisualization.files_path' +&& mv '$ovisualization.files_path/index.html' '$ovisualization' + + ]]></command> + <inputs> + <param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm1" optional="False" type="data" /> + <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm2" optional="False" type="data" /> + <param label="--p-method: " name="pmethod" optional="True" type="select"> + <option selected="True" value="None">Selection is Optional</option> + <option value="spearman">spearman</option> + <option value="pearson">pearson</option> + </param> + <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" min="0" name="ppermutations" optional="True" type="integer" value="999" /> + <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean" /> + <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: \'Distance Matrix 1\']" name="plabel1" optional="False" type="text" value="\'Distance Matrix 1\'" /> + <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: \'Distance Matrix 2\']" name="plabel2" optional="False" type="text" value="\'Distance Matrix 2\'" /> + <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" /> + + </inputs> + + <outputs> + <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" /> + + </outputs> + + <help><![CDATA[ +Apply the Mantel test to two distance matrices +############################################################### + +Apply a two-sided Mantel test to identify correlation between two distance +matrices. Note: the directionality of the comparison has no bearing on the +results. Thus, comparing distance matrix X to distance matrix Y is +equivalent to comparing Y to X. Note: the order of samples within the two +distance matrices does not need to be the same; the distance matrices will +be reordered before applying the Mantel test. See the scikit-bio docs for +more details about the Mantel test: http://scikit- +bio.org/docs/latest/generated/skbio.stats.distance.mantel + +Parameters +---------- +dm1 : DistanceMatrix + Matrix of distances between pairs of samples. +dm2 : DistanceMatrix + Matrix of distances between pairs of samples. +method : Str % Choices('spearman', 'pearson'), optional + The correlation test to be applied in the Mantel test. +permutations : Int % Range(0, None), optional + The number of permutations to be run when computing p-values. Supplying + a value of zero will disable permutation testing and p-values will not + be calculated (this results in *much* quicker execution time if + p-values are not desired). +intersect_ids : Bool, optional + If supplied, IDs that are not found in both distance matrices will be + discarded before applying the Mantel test. Default behavior is to error + on any mismatched IDs. +label1 : Str, optional + Label for `dm1` in the output visualization. +label2 : Str, optional + Label for `dm2` in the output visualization. + +Returns +------- +visualization : Visualization + ]]></help> + <macros> + <import>qiime_citation.xml</import> + </macros> + <expand macro="qiime_citation"/> +</tool> \ No newline at end of file