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comparison make_otu_heatmap.xml @ 0:c1bd0c560018 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime commit bcbe76277f3e60303faf826f8ce7f018bc663a9a-dirty
author bebatut
date Tue, 02 Feb 2016 05:50:37 -0500
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1 <tool id="qiime_make_otu_heatmap" name="make otu heatmap" version="1.9.1galaxy1">
2 <description>Plot heatmap of OTU table</description>
3
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7
8 <expand macro="requirements" />
9
10 <command>
11 <![CDATA[
12 make_otu_heatmap.py
13 -i $otu_table_fp
14 -o make_otu_heatmap_output
15
16 #if str($otu_tree) != 'None':
17 -t $otu_tree
18 #end if
19
20 #if str($map_fname) != 'None':
21 -m $map_fname
22 #end if
23
24 #if str($category):
25 -c $category
26 #end if
27
28 #if str($sample_tree) != 'None':
29 -s $sample_tree
30 #end if
31
32 #if $no_log_transform:
33 --no_log_transform
34 #end if
35
36 #if $suppress_row_clustering:
37 --suppress_row_clustering
38 #end if
39
40 #if $suppress_column_clustering:
41 --suppress_column_clustering
42 #end if
43
44 #if $absolute_abundance:
45 --absolute_abundance
46 #end if
47
48 #if str($ad.select) == "yes":
49 #if $ad.color_scheme:
50 --color_scheme $ad.color_scheme
51 #end if
52
53 #if $ad.width:
54 --width $ad.width
55 #end if
56
57 #if $ad.height:
58 --height $ad.height
59 #end if
60
61 #if $ad.dpi:
62 --dpi $ad.dpi
63 #end if
64
65 #if $ad.obs_md_category:
66 --obs_md_category $ad.obs_md_category
67 #end if
68
69 #if $ad.obs_md_level:
70 --obs_md_level $ad.obs_md_level
71 #end if
72 #end if
73 ]]>
74
75 </command>
76
77 <inputs>
78 <param label="-i/--otu_table_fp: path to the input OTU table (i.e., the
79 output from make_otu_table.py)" name="otu_table_fp" optional="False"
80 type="data"/>
81 <param default="None" label="-t/--otu_tree: Tree file to be used for
82 sorting OTUs in the heatmap" name="otu_tree" optional="True"
83 type="data"/>
84 <param default="None" label="-m/--map_fname: Metadata mapping file to be
85 used for sorting Samples in the heatmap." name="map_fname" optional="True"
86 type="data"/>
87 <param default="None" label="-c/--category: Metadata category for sorting
88 samples. Samples will be clustered within each category level using
89 euclidean UPGMA." name="category" optional="True" type="text"/>
90 <param default="None" label="-s/--sample_tree: Tree file to be used for
91 sorting samples (e.g, output from upgma_cluster.py). If both this and
92 the sample mapping file are provided, the mapping file is ignored."
93 name="sample_tree" optional="True" type="data"/>
94 <param label="--no_log_transform: Data will not be log-transformed. Without
95 this option, all zeros will be set to a small value (default is 1/2
96 the smallest non-zero entry). Data will be translated to be non-negative
97 after log transform, and num_otu_hits will be set to 0."
98 name="no_log_transform" selected="False" type="boolean"/>
99 <param label="--suppress_row_clustering: No UPGMA clustering of OTUs (rows)
100 is performed. If --otu_tree is provided, this flag is ignored."
101 name="suppress_row_clustering" selected="False" type="boolean"/>
102 <param label="--suppress_column_clustering: No UPGMA clustering of Samples
103 (columns) is performed. If --map_fname is provided, this flag is ignored."
104 name="suppress_column_clustering" selected="False" type="boolean"/>
105 <param label="--absolute_abundance: Do not normalize samples to sum to 1.
106 [default False]" name="absolute_abundance" selected="False"
107 type="boolean"/>
108
109 <conditional name="ad">
110 <param name="select" type="select" label="Show advanced options">
111 <option value="no" selected="True">No</option>
112 <option value="yes">Yes</option>
113 </param>
114 <when value="no">
115 </when>
116 <when value="yes">
117 <param default="YlGn" label="Color scheme for figure. see http://matplotlib.org/examples/color/colormaps_reference.html for choices [default: YlGn]"
118 name="color_scheme" optional="True" type="text"/>
119 <param default="5" label="Width of the figure in inches [default: 5]"
120 name="width" optional="True" type="text"/>
121 <param default="5" label="Height of the figure in inches [default: 5]"
122 name="height" optional="True" type="text"/>
123 <param label="Resolution of the figure in dots per inch [default:
124 value of savefig.dpi in matplotlibrc file]" name="dpi"
125 optional="True" type="text"/>
126 <param label="Observation metadata category to plot [default: taxonomy]"
127 name="obs_md_category" optional="True" type="data"/>
128 <param label="The level of observation metadata to plot for hierarchical
129 metadata [default: lowest level]" name="obs_md_level" optional="True"
130 type="data"/>
131 </when>
132 </conditional>
133 </inputs>
134
135 <outputs>
136 <data format="pdf" from_work_dir="make_otu_heatmap_output" name="heatmap_OTU"
137 label="heatmap_OTU.pdf"/>
138 </outputs>
139
140 <tests>
141 <test>
142 </test>
143 </tests>
144
145 <help><![CDATA[
146
147 **What it does**
148
149 This script visualizes an OTU table as a heatmap where each row corresponds to an
150 OTU and each column corresponds to a sample. The higher the relative abundance of
151 an OTU in a sample, the more intense the color at the corresponsing position in
152 the heatmap. By default, the OTUs (rows) will be clustered by UPGMA hierarchical
153 clustering, and the samples (columns) will be presented in the order in which
154 they appear in the OTU table. Alternatively, the user may supply a tree to sort
155 the OTUs (rows) or samples (columns), or both. The user may also pass in a mapping
156 file for sorting samples. If the user passes in a mapping file and a metadata
157 category, samples (columns) will be grouped by category value and subsequently
158 clustered within each group.
159 A single output file is created containing the heatmap of the OTU table (a PDF
160 file by default).
161 ]]>
162 </help>
163
164 <citations>
165 <expand macro="citations" />
166 </citations>
167 </tool>