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comparison hierarchical_clustering_heatmap.xml @ 1:2e7d47c0b027 draft

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"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author malex
date Mon, 08 Mar 2021 22:04:06 +0000
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0:b54326490b4d 1:2e7d47c0b027
1 <tool id="secimtools_hierarchical_clustering_heatmap" name="Hierarchical Clustering Heatmap" version="@WRAPPER_VERSION@">
2 <description>- Calculate means per group and plot a heatmap.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 hierarchical_clustering_heatmap.py
9 --input $input
10 --design $design
11 --uniqID $uniqID
12 #if $dendogram
13 --dendogram
14 #end if
15 --labels $labels
16 --fig $fig
17 ]]></command>
18 <inputs>
19 <param name="input" type="data" format="tabular" label="Wide Dataset" help="Input your tab-separated wide format dataset. If not tab separated see TIP below."/>
20 <param name="design" type="data" format="tabular" label="Design File" help="Input your design file (tab-separated). Note you need a 'sampleID' column. If not tab separated see TIP below."/>
21 <param name="uniqID" type="text" size="30" value="" label="Unique Feature ID" help="Name of the column in your wide dataset that has unique identifiers."/>
22 <param name="dendogram" type="boolean" value="False" label="Add dendogram on heatmap" help="Select 'Yes' to print a dendogram over the heatmap."/>
23 <param name="labels" type="select" label="Select to remove labels from plots" multiple="true" display="checkboxes">
24 <option value="x">X-axis labels</option>
25 <option value="y">Y-axis labels</option>
26 </param>
27 </inputs>
28 <outputs>
29 <data format="pdf" name="fig" label="${tool.name} on ${on_string}"/>
30 </outputs>
31 <tests>
32 <test>
33 <param name="input" value="ST000006_data.tsv"/>
34 <param name="design" value="ST000006_design.tsv"/>
35 <param name="uniqID" value="Retention_Index" />
36 <param name="dendogram" value="True" />
37 <param name="labels" value="x,y" />
38 <output name="fig" file="ST000006_hierarchical_clustering_heatmap_figure.pdf" compare="sim_size" delta="10000" />
39 </test>
40 </tests>
41 <help><![CDATA[
42
43 @TIP_AND_WARNING@
44
45 **Tool Description**
46
47 This tool generates a hierarchical cluster heatmap from a wide format dataset.
48 An option to add a hierarchical clustering dendrogram on the top of the heatmap figure is included along with an option to removal plot labels.
49
50 **NOTE:** This script works best with log transformed data that contains no missing data.
51
52 --------------------------------------------------------------------------------
53
54 **Input**
55
56 - Two input datasets are required.
57
58 @WIDE@
59
60 **NOTE:** The sample IDs must match the sample IDs in the Design File
61 (below). Extra columns will automatically be ignored.
62
63
64 @METADATA@
65
66 **In addition to your datasets, you need to provide:**
67
68 **Unique Feature ID**
69
70 - The column name in your wide dataset that contains the unique IDs for
71 your features. In our example dataset you would input *Compound*.
72
73 --------------------------------------------------------------------------------
74
75 **Output**
76
77 A PDF file with a hierarchical cluster heatmap of the data
78
79 ]]></help>
80 <expand macro="citations"/>
81 </tool>