annotate clustergrammerIPG.xml @ 1:c90127c2a1ae draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
author azomics
date Sun, 27 Jun 2021 22:13:16 +0000
parents fee56ee2f7ac
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
c90127c2a1ae "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit e47edffe14c2e8544fe0d00d932090657beae528"
azomics
parents: 0
diff changeset
1 <tool id="clustergrammer_flow" name="Generate a heat map" version="1.1+galaxy1" profile="18.01">
0
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
2 <description>of a flow analysis using Clustergrammer</description>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
3 <requirements>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
4 <requirement type="package" version="2.11.2">jinja2</requirement>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
5 <requirement type="package" version="1.13.6">clustergrammer</requirement>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
6 </requirements>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
7 <stdio>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
8 <exit_code range="1"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
9 <exit_code range="2" level="fatal" description="Please provide a comma-separated list of indices." />
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
10 <exit_code range="3" level="fatal" description="Please provide integer as indices." />
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
11 <exit_code range="4" level="fatal" description="Indices within one of the categories are used several times." />
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
12 <exit_code range="5" level="fatal" description="Please provide indices within the range of your input matrix." />
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
13 <exit_code range="6:"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
14 </stdio>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
15 <command><![CDATA[
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
16 python '$__tool_directory__/clustergrammerIPG.py' '${input_matrix}' '${html_file}' '${html_file.files_path}' '$__tool_directory__' '${dist_type}' '${linkage}'
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
17 #for $category in $cat
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
18 'new_cat'
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
19 '${category.roc}'
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
20 '${category.cat_title}'
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
21 '${category.label1}'
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
22 '${category.indices1}'
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
23 #for $catlabel in $category.cat_labels
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
24 'new_label'
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
25 '${catlabel.label}'
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
26 '${catlabel.indices}'
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
27 #end for
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
28 #end for
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
29 ;
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
30 cp -r '$__tool_directory__'/js '${html_file.files_path}'/;
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
31 cp -r '$__tool_directory__'/css '${html_file.files_path}'/;
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
32 ]]>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
33 </command>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
34 <inputs>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
35 <param format="flowmfi" name="input_matrix" type="data" label="Centroids file" help="Any type of input matrix can be used."/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
36 <param name="dist_type" type="select" label="Clustering option - Compute distance using:" help="See below for documentation, default is set to cosine.">
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
37 <option value="cosine" selected="true">Cosine</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
38 <option value="euclidean">Euclidian</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
39 <option value="correlation">Correlation</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
40 <option value="jaccard">Jaccard</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
41 </param>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
42 <param name="linkage" type="select" label="Clustering option - Linkage type" help="See below for documentation. default is set to average.">
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
43 <option value="average" selected="true">Average</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
44 <option value="single">Single</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
45 <option value="complete">Complete</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
46 <option value="weighted">Weigthed</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
47 </param>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
48 <repeat name="cat" title="Category">
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
49 <param name="roc" type="select" label="Is this category for row data or column data?">
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
50 <option value="row" selected="true">Row data (population or cluster)</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
51 <option value="col">Column (marker name)</option>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
52 </param>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
53 <param name="cat_title" type="text" label="Category Title" value="i.e.: Marker Type"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
54 <param name="label1" type="text" label="Category label" value="i.e.: Surface Marker"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
55 <param name="indices1" type="text" label="Indices of rows or columns this label should be given to." value="i.e.:1,2,5"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
56 <repeat name="cat_labels" title="Category label">
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
57 <param name="label" type="text" label="Category label" value="i.e.: Phospho Marker"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
58 <param name="indices" type="text" label="Indices of rows or columns this label should be given to." value="i.e.:3,6,7"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
59 </repeat>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
60 </repeat>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
61 </inputs>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
62 <outputs>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
63 <data format="html" name="html_file" label="Heatmap of ${input_matrix.name}"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
64 </outputs>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
65 <tests>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
66 <test>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
67 <param name="input_matrix" value="test.flowmfi"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
68 <output name="html_file" file="heatmap.html">
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
69 <extra_files type="file" name="mult_view.json" value="mult_view.json"/>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
70 </output>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
71 </test>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
72 </tests>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
73 <help><![CDATA[
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
74 This tool generates a heat map from the provided input matrix using Clustergrammer.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
75
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
76 -----
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
77
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
78 **Input**
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
79
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
80 Please provide a tab-separated matrix of values as input, for instance a centroid file from a FLOCK analysis.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
81 Rows and columns can be annotated by setting up categories and labels for each group within categories.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
82
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
83 .. class:: infomark
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
84
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
85 Any type of matrix can be used but the datatype expected by this tool is flowmfi. You can modify the file format of any file in your history by clicking on the pencil next to the name of your file, and going to the 'Datatype' tab.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
86
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
87 **Distance and Linkage types**
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
88
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
89 Distance_ and linkage_ are computed using functions implemented in SciPy. Please refer to their documentation for further explanations.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
90
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
91 **Graphical output**
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
92
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
93 The output is an interactive heat-map of the matrix provided.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
94
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
95 .. class:: warningmark
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
96
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
97 The color scale represents ranges of fluorescence intensity and covers values between the minimun and maximum intensity values in the dataset used as input.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
98
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
99 .. class:: infomark
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
100
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
101 Some features might not show up depending on the browser used. If the dendograms aren't displayed, try opening the output in Chrome.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
102
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
103 -----
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
104
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
105 **Example**
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
106
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
107 *Input*: Centroids file::
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
108
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
109 Population Marker1 Marker2 Marker3
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
110 1 38 49 10
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
111 2 21 63 100
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
112 3 31 52 45
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
113 4 11 78 25
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
114
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
115 *Interactive Graphical output*
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
116
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
117 .. image:: ./static/images/flowtools/clustergrammer.png
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
118
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
119 -----
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
120
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
121 Clustergrammer_ is a project from the Ma'ayan lab. Find them on GitHub_, more info here_.
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
122
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
123 .. _Clustergrammer: http://amp.pharm.mssm.edu/clustergrammer/
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
124 .. _GitHub: https://github.com/MaayanLab/clustergrammer
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
125 .. _here: https://clustergrammer.readthedocs.io/getting_started.html
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
126 .. _Distance: https://docs.scipy.org/doc/scipy/reference/spatial.distance.html
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
127 .. _linkage: https://docs.scipy.org/doc/scipy/reference/generated/scipy.cluster.hierarchy.linkage.html#scipy.cluster.hierarchy.linkage
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
128 ]]>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
129 </help>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
130 <citations>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
131 <citation type="doi">10.1038/sdata.2017.151</citation>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
132 </citations>
fee56ee2f7ac "planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/clustergrammer_flow commit b11dfcf10d287c1da91ffb1d5d0148c7f8f61356"
azomics
parents:
diff changeset
133 </tool>