Mercurial > repos > malex > secimtools
comparison hierarchical_clustering_heatmap.xml @ 1:2e7d47c0b027 draft
"planemo upload for repository https://malex@toolshed.g2.bx.psu.edu/repos/malex/secimtools"
author | malex |
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date | Mon, 08 Mar 2021 22:04:06 +0000 |
parents | |
children | caba07f41453 |
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0:b54326490b4d | 1:2e7d47c0b027 |
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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> |