Mercurial > repos > bebatut > metaphlan2

annotate metaphlan_hclust_heatmap.xml @ 32:c941148c75c7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 9e93b527d3cc9023467b1b285b068dac21b0727b-dirty
author bebatut
date Wed, 22 Feb 2017 03:49:35 -0500
parents 83f06bee818c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
1 <tool id="metaphlan2_metaphlan_hclust_heatmap" name="Generate heatmap" version="@WRAPPER_VERSION@.0">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
2
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
3 <description>with hierarchical clustering of both samples
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
4 and microbial clades for MetaPhlAn2</description>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
5
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
6 <macros>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
7 <import>metaphlan2_macros.xml</import>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
8 </macros>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
9
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
10 <expand macro="requirements"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
11 <expand macro="stdio"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
12
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
13 <version_command>metaphlan_hclust_heatmap.py -v</version_command>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
14
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
15 <command>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
16 <![CDATA[
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
17 metaphlan_hclust_heatmap.py
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
18 --in '$in'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
19
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
20 #if $output_format == "png"
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
21 --out 'output.png'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
22 #else if $output_format == "pdf"
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
23 --out 'output.pdf'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
24 #else if $output_format == "svg"
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
25 --out 'output.svg'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
26 #end if
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
27
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
28 -m '$m'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
29 -d '$d'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
30 -f '$f'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
32 #if $x
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
33 -x '$x'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
34 #end if
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
35 #if $y
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
36 -y '$y'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
37 #end if
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
38 --minv '$minv'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
39 #if $maxv
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
40 --maxv $maxv
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
41 #end if
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
42 --tax_lev '$tax_lev'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
43 --perc '$perc'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
44 #if $top
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
45 --top '$top'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
46 #end if
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
47 --sdend_h '$sdend_h'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
48 --fdend_w '$fdend_w'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
49 --cm_h '$cm_h'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
50 --font_size '$font_size'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
51 --clust_line_w '$clust_line_w'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
52 -c '$c'
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
53 ]]>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
54 </command>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
55
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
56 <inputs>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
57 <param argument="--in" type="data" format="tabular,txt" label="Input file of microbial relative abundances" help="This file is typically obtained with merge_metaphlan_tables"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
58 <param name="output_format" type="select" label="Format for the output image">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
59 <option value="png" selected="true">PNG</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
60 <option value="pdf">PDF</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
61 <option value="svg">SVG</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
62 </param>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
63 <param argument="-m" type="select" label="Hierarchical clustering method">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
64 <option value="average" selected="true">Average</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
65 <option value="centroid">Centroid</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
66 <option value="complete">Complete</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
67 <option value="median">Median</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
68 <option value="single">Single</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
69 <option value="ward">Ward</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
70 <option value="weighted">Weighted</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
71 </param>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
72 <param argument="-d" type="select" label="Distance function for samples">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
73 <option value="braycurtis" selected="true">braycurtis</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
74 <option value="canberra">canberra</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
75 <option value="chebyshev">chebyshev</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
76 <option value="cityblock">cityblock</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
77 <option value="correlation">correlation</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
78 <option value="cosine">cosine</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
79 <option value="dice">dice</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
80 <option value="euclidean">euclidean</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
81 <option value="hamming">hamming</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
82 <option value="jaccard">jaccard</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
83 <option value="kulsinski">kulsinski</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
84 <option value="mahalanobis">mahalanobis</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
85 <option value="matching">matching</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
86 <option value="minkowski">minkowski</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
87 <option value="rogerstanimoto">rogerstanimoto</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
88 <option value="russellrao">russellrao</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
89 <option value="seuclidean">seuclidean</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
90 <option value="sokalmichener">sokalmichener</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
91 <option value="sokalsneath">sokalsneath</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
92 <option value="sqeuclidean">sqeuclidean</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
93 <option value="wminkowski">wminkowski</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
94 <option value="ward">ward</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
95 <option value="yule">yule</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
96 </param>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
97 <param argument="-f" type="select" label="Distance function for microbes">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
98 <option value="braycurtis">braycurtis</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
99 <option value="canberra">canberra</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
100 <option value="chebyshev">chebyshev</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
101 <option value="cityblock">cityblock</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
102 <option value="correlation" selected="true">correlation</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
103 <option value="cosine">cosine</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
104 <option value="dice">dice</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
105 <option value="euclidean">euclidean</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
106 <option value="hamming">hamming</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
107 <option value="jaccard">jaccard</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
108 <option value="kulsinski">kulsinski</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
109 <option value="mahalanobis">mahalanobis</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
110 <option value="matching">matching</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
111 <option value="minkowski">minkowski</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
112 <option value="rogerstanimoto">rogerstanimoto</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
113 <option value="russellrao">russellrao</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
114 <option value="seuclidean">seuclidean</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
115 <option value="sokalmichener">sokalmichener</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
116 <option value="sokalsneath">sokalsneath</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
117 <option value="sqeuclidean">sqeuclidean</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
118 <option value="wminkowski">wminkowski</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
119 <option value="ward">ward</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
120 <option value="yule">yule</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
121 </param>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
122 <param argument="-x" type="integer" optional="True" label="Width of heatmap cells" help="Automatically set, this option should not be necessary unless for very large heatmaps"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
123 <param argument="-y" type="integer" optional="True" label="Height of heatmap cells" help="Automatically set, this option should not be necessary unless for very large heatmaps"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
124 <param argument="--minv" type="float" value="0" label="Minimum value to display" help="Values around 0.001 are also reasonable"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
125 <param argument="--maxv" type="float" optional="True" label="Maximum value to display" help="Default is maximum value present, can be set e.g. to 100 to display the full scale"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
126 <param argument="--tax_lev" type="select" label="Taxonomic level to display">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
127 <option value="a">All taxonomic levels</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
128 <option value="k">Kingdoms (Bacteria and Archaea) only</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
129 <option value="p">Phyla only</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
130 <option value="c">Classes only</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
131 <option value="o">Orders only</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
132 <option value="f">Families only</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
133 <option value="g">Genera only</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
134 <option value="s" selected="true">Species only</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
135 </param>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
136 <param argument="--perc" type="integer" value="90" label="Percentile to be used for ordering the microbes"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
137 <param argument="--top" type="integer" optional="True" label="Number of most abundant microbes to display"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
138 <param argument="--sdend_h" type="float" value="0.1" label="Height of the sample dendrogram"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
139 <param argument="--fdend_w" type="float" value="0.1" label="Width of the sample dendrogram"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
140 <param argument="--cm_h" type="float" value="0.03" label="Height of the colormap"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
141 <param argument="--font_size" type="integer" value="7" label="Label font sizes"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
142 <param argument="--clust_line_w" type="float" value="" label="Line width for the dendrograms"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
143 <param argument="-c" type="select" label="Taxonomic level to display">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
144 <option value="autumn">autumn</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
145 <option value="bbcyr">bbcyr</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
146 <option value="bbcry">bbcry</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
147 <option value="binary">binary</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
148 <option value="Blues">Blues</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
149 <option value="bone">bone</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
150 <option value="BrBG">BrBG</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
151 <option value="brg">brg</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
152 <option value="BuGn">BuGn</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
153 <option value="BuPu">BuPu</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
154 <option value="bwr">bwr</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
155 <option value="cool">cool</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
156 <option value="copper">copper</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
157 <option value="gist_earth">gist_earth</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
158 <option value="gist_ncar">gist_ncar</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
159 <option value="gist_rainbow">gist_rainbow</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
160 <option value="gist_stern">gist_stern</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
161 <option value="GnBu">GnBu</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
162 <option value="gray">gray</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
163 <option value="Greys">Greys</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
164 <option value="hot">hot</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
165 <option value="hsv">hsv</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
166 <option value="jet" selected="true">jet</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
167 <option value="OrRd">OrRd</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
168 <option value="Oranges">Oranges</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
169 <option value="PRGn">PRGn</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
170 <option value="pink">pink</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
171 <option value="PiYG">PiYG</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
172 <option value="PuBu">PuBu</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
173 <option value="PuBuGn">PuBuGn</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
174 <option value="PuOr">PuOr</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
175 <option value="PuRd">PuRd</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
176 <option value="Purples">Purples</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
177 <option value="RdBu">RdBu</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
178 <option value="RdGy">RdGy</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
179 <option value="RdPu">RdPu</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
180 <option value="RdYlBu">RdYlBu</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
181 <option value="RdYlGn">RdYlGn</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
182 <option value="Reds">Reds</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
183 <option value="seismic">seismic</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
184 <option value="spectral">spectral</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
185 <option value="Spectral">Spectral</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
186 <option value="spring">spring</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
187 <option value="summer">summer</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
188 <option value="terrain">terrain</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
189 <option value="winter">winter</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
190 <option value="YlGn">YlGn</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
191 <option value="YlGnBu">YlGnBu</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
192 <option value="YlOrBr">YlOrBr</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
193 <option value="YlOrRd">YlOrRd</option>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
194 </param>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
195 </inputs>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
196
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
197 <outputs>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
198 <data format="pdf" name="out_pdf" from_work_dir="output.pdf" label="${tool.name} on ${on_string}">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
199 <filter>output_format == "pdf"</filter>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
200 </data>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
201 <data format="png" name="out_png" from_work_dir="output.png" label="${tool.name} on ${on_string}">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
202 <filter>output_format == "png"</filter>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
203 </data>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
204 <data format="svg" name="out_svg" from_work_dir="output.svg" label="${tool.name} on ${on_string}">
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
205 <filter>output_format == "svg"</filter>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
206 </data>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
207 </outputs>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
208
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
209 <tests>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
210 <test>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
211 <param name="in" value="merged_community_profile.tabular"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
212 <param name="output_format" value="png"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
213 <param name="m" value="average"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
214 <param name="d" value="braycurtis"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
215 <param name="f" value="correlation"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
216 <param name="minv" value="0"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
217 <param name="tax_lev" value="a"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
218 <param name="perc" value="90"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
219 <param name="sdend_h" value="0.1"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
220 <param name="fdend_w" value="0.1"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
221 <param name="cm_h" value="0.03"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
222 <param name="font_size" value="7"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
223 <param name="clust_line_w" value="1"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
224 <param name="c" value="jet"/>
32
c941148c75c7 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 9e93b527d3cc9023467b1b285b068dac21b0727b-dirty
bebatut
parents: 31
diff changeset
225 <output name="out_png" file="heatmap.png" ftype="png" compare="sim_size"/>
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
226 </test>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
227 <test>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
228 <param name="in" value="merged_community_profile.tabular"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
229 <param name="output_format" value="pdf"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
230 <param name="m" value="ward"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
231 <param name="d" value="euclidean"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
232 <param name="f" value="euclidean"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
233 <param name="minv" value="0"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
234 <param name="tax_lev" value="a"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
235 <param name="perc" value="90"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
236 <param name="sdend_h" value="0.1"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
237 <param name="fdend_w" value="0.1"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
238 <param name="cm_h" value="0.03"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
239 <param name="font_size" value="7"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
240 <param name="clust_line_w" value="1"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
241 <param name="c" value="pink"/>
32
c941148c75c7 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 9e93b527d3cc9023467b1b285b068dac21b0727b-dirty
bebatut
parents: 31
diff changeset
242 <output name="out_pdf" file="heatmap.pdf" compare="sim_size"/>
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
243 </test>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
244 <test>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
245 <param name="in" value="merged_community_profile.tabular"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
246 <param name="output_format" value="svg"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
247 <param name="m" value="complete"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
248 <param name="d" value="hamming"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
249 <param name="f" value="matching"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
250 <param name="minv" value="0"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
251 <param name="tax_lev" value="a"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
252 <param name="perc" value="90"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
253 <param name="sdend_h" value="0.1"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
254 <param name="fdend_w" value="0.1"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
255 <param name="cm_h" value="0.03"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
256 <param name="font_size" value="7"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
257 <param name="clust_line_w" value="1"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
258 <param name="c" value="pink"/>
32
c941148c75c7 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit 9e93b527d3cc9023467b1b285b068dac21b0727b-dirty
bebatut
parents: 31
diff changeset
259 <output name="out_svg" file="heatmap.svg" ftype="svg" compare="sim_size"/>
31
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
260 </test>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
261 </tests>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
262
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
263 <help><![CDATA[
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
264
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
265 **What it does**
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
266
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
267 MetaPhlAn is a computational tool to profile the structure and the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data with species level resolution. For more information, check the `user manual <https://bitbucket.org/biobakery/metaphlan2/>`_.
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
268
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
269 This tool generates heatmaps with hierarchical clustering of both samples
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
270 and microbial clades. The script can also subsample the number of clades to
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
271 display based on the their nth percentile abundance value in each sample
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
272
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
273 ]]></help>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
274
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
275 <expand macro="citations"/>
83f06bee818c planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/metaphlan2/ commit a6bf1721b4efa39b8cbcd059288c68e4abf8f9bd-dirty
bebatut
parents:
diff changeset
276 </tool>