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comparison qiime2/qiime_diversity_mantel.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_diversity_mantel" name="qiime diversity mantel" version="2019.7"> 2 <tool id="qiime_diversity_mantel" name="qiime diversity mantel"
3 <description> - Apply the Mantel test to two distance matrices</description> 3 version="2020.8">
4 <requirements> 4 <description>Apply the Mantel test to two distance matrices</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime diversity mantel 9 qiime diversity mantel
9 10
10 --i-dm1=$idm1 11 --i-dm1=$idm1
12
11 --i-dm2=$idm2 13 --i-dm2=$idm2
12 14
13 #if str($pmethod) != 'None': 15 #if str($pmethod) != 'None':
14 --p-method=$pmethod 16 --p-method=$pmethod
15 #end if 17 #end if
16 18
17 #if str($ppermutations): 19 --p-permutations=$ppermutations
18 --p-permutations=$ppermutations
19 #end if
20 20
21 #if $pintersectids: 21 #if $pintersectids:
22 --p-intersect-ids 22 --p-intersect-ids
23 #end if 23 #end if
24 24
25 #if str($plabel1):
26 --p-label1=$plabel1
27 #end if
28 #if str($plabel2):
29 --p-label2=$plabel2
30 #end if
31 --o-visualization=ovisualization
25 32
26 33 #if str($examples) != 'None':
27 #if '__sq__' in str($plabel1): 34 --examples=$examples
28 #set $plabel1_temp = $plabel1.replace('__sq__', "'")
29 #set $plabel1 = $plabel1_temp
30 #end if 35 #end if
31 36
32 #if str($plabel1): 37 ;
33 --p-label1="$plabel1" 38 cp ofiltereddistancematrix.qza $ofiltereddistancematrix
34 #end if
35 39
40 ;
41 qiime tools export ovisualization.qzv --output-path out
42 && mkdir -p '$ovisualization.files_path'
43 && cp -r out/* '$ovisualization.files_path'
44 && mv '$ovisualization.files_path/index.html' '$ovisualization'
36 45
46 ]]></command>
47 <inputs>
48 <param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm1" optional="False" type="data" />
49 <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm2" optional="False" type="data" />
50 <param label="--p-method: " name="pmethod" optional="True" type="select">
51 <option selected="True" value="None">Selection is Optional</option>
52 <option value="spearman">spearman</option>
53 <option value="pearson">pearson</option>
54 </param>
55 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" min="0" name="ppermutations" optional="True" type="integer" value="999" />
56 <param label="--p-intersect-ids: --p-intersect-ids: / --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean" />
57 <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: \'Distance Matrix 1\']" name="plabel1" optional="False" type="text" value="\'Distance Matrix 1\'" />
58 <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: \'Distance Matrix 2\']" name="plabel2" optional="False" type="text" value="\'Distance Matrix 2\'" />
59 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
60
61 </inputs>
37 62
38 #if '__sq__' in str($plabel2): 63 <outputs>
39 #set $plabel2_temp = $plabel2.replace('__sq__', "'") 64 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
40 #set $plabel2 = $plabel2_temp 65
41 #end if 66 </outputs>
42 67
43 #if str($plabel2): 68 <help><![CDATA[
44 --p-label2="$plabel2"
45 #end if
46
47
48
49 --o-visualization=ovisualization
50 ;
51 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
52 && cp -r out/* '$ovisualization.files_path'
53 && mv '$ovisualization.files_path/index.html' '$ovisualization';
54 ]]></command>
55 <inputs>
56 <param format="qza,no_unzip.zip" label="--i-dm1: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm1" optional="False" type="data"/>
57 <param format="qza,no_unzip.zip" label="--i-dm2: ARTIFACT Matrix of distances between pairs of samples. DistanceMatrix [required]" name="idm2" optional="False" type="data"/>
58 <param label="--p-method: " name="pmethod" optional="True" type="select">
59 <option selected="True" value="None">Selection is Optional</option>
60 <option value="spearman">spearman</option>
61 <option value="pearson">pearson</option>
62 </param>
63 <param label="--p-permutations: INTEGER Range(0, None) The number of permutations to be run when computing p-values. Supplying a value of zero will disable permutation testing and p-values will not be calculated (this results in *much* quicker execution time if p-values are not desired). [default: 999]" name="ppermutations" optional="True" type="integer" min="0" value="999"/>
64 <param label="--p-intersect-ids: --p-no-intersect-ids If supplied, IDs that are not found in both distance matrices will be discarded before applying the Mantel test. Default behavior is to error on any mismatched IDs. [default: False]" name="pintersectids" selected="False" type="boolean"/>
65 <param label="--p-label1: TEXT Label for `dm1` in the output visualization. [default: 'Distance Matrix 1']" name="plabel1" optional="True" type="text" value="Distance Matrix 1"/>
66 <param label="--p-label2: TEXT Label for `dm2` in the output visualization. [default: 'Distance Matrix 2']" name="plabel2" optional="True" type="text" value="Distance Matrix 2"/>
67 </inputs>
68 <outputs>
69 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
70 </outputs>
71 <help><![CDATA[
72 Apply the Mantel test to two distance matrices 69 Apply the Mantel test to two distance matrices
73 ############################################## 70 ###############################################################
74 71
75 Apply a two-sided Mantel test to identify correlation between two distance 72 Apply a two-sided Mantel test to identify correlation between two distance
76 matrices. Note: the directionality of the comparison has no bearing on the 73 matrices. Note: the directionality of the comparison has no bearing on the
77 results. Thus, comparing distance matrix X to distance matrix Y is 74 results. Thus, comparing distance matrix X to distance matrix Y is
78 equivalent to comparing Y to X. Note: the order of samples within the two 75 equivalent to comparing Y to X. Note: the order of samples within the two
79 distance matrices does not need to be the same; the distance matrices will 76 distance matrices does not need to be the same; the distance matrices will
80 be reordered before applying the Mantel test. See the scikit-bio docs for 77 be reordered before applying the Mantel test. See the scikit-bio docs for
81 more details about the Mantel test: http://scikit- 78 more details about the Mantel test: http://scikit-
82 bio.org/docs/latest/generated/generated/skbio.stats.distance.mantel.html 79 bio.org/docs/latest/generated/skbio.stats.distance.mantel
83 80
84 Parameters 81 Parameters
85 ---------- 82 ----------
86 dm1 : DistanceMatrix 83 dm1 : DistanceMatrix
87 Matrix of distances between pairs of samples. 84 Matrix of distances between pairs of samples.
104 Label for `dm2` in the output visualization. 101 Label for `dm2` in the output visualization.
105 102
106 Returns 103 Returns
107 ------- 104 -------
108 visualization : Visualization 105 visualization : Visualization
109 ]]></help> 106 ]]></help>
110 <macros> 107 <macros>
111 <import>qiime_citation.xml</import> 108 <import>qiime_citation.xml</import>
112 </macros> 109 </macros>
113 <expand macro="qiime_citation"/> 110 <expand macro="qiime_citation"/>
114 </tool> 111 </tool>