Mercurial > repos > imgteam > libcarna_render

annotate render.xml @ 4:a9f10dceb17e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
author imgteam
date Tue, 13 Jan 2026 12:21:55 +0000
parents 31a2e1909ae5
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
1 <tool id="libcarna_render" name="Render 3-D image data" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
2 <description>with LibCarna</description>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
3 <macros>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
4 <import>creators.xml</import>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
5 <import>validators.xml</import>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
6 <import>colormaps.xml</import>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
7 <token name="@TOOL_VERSION@">0.2.0</token>
4
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
8 <token name="@VERSION_SUFFIX@">2</token>
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
9 <xml name="params/intensity" tokens="name,label,value,help" token_help="">
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
10 <section name="@NAME@" title="@LABEL@" expanded="true" help="@HELP@">
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
11 <param name="type" type="select" label="Type of the intensity value"
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
12 help="For relative intensity values, 0 is the minimum intensity of the image, and 1 is the maximum intensity.">
1
22618ff03b3d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 6f0441e7c72176aaa13ffc14988162628ae2a0d6
imgteam
parents: 0
diff changeset
13 <option value="absolute">Absolute intensity value</option>
22618ff03b3d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 6f0441e7c72176aaa13ffc14988162628ae2a0d6
imgteam
parents: 0
diff changeset
14 <option value="relative" selected="true">Relative intensity value</option>
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
15 </param>
1
22618ff03b3d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 6f0441e7c72176aaa13ffc14988162628ae2a0d6
imgteam
parents: 0
diff changeset
16 <param name="value" type="float" value="@VALUE@" label="Intensity value"/>
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
17 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
18 </xml>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
19 <xml name="params/builtin_cmap">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
20 <conditional name="ramp">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
21 <param name="enabled" type="select" label="Ramp function"
3
31a2e1909ae5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065
imgteam
parents: 2
diff changeset
22 help="Use a piecewise linear ramp function for the alpha channel of the color map.">
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
23 <option value="false" selected="true">Disabled</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
24 <option value="true">Enabled</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
25 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
26 <when value="true">
4
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
27 <expand macro="params/intensity" name="start" value="0" label="Ramp start"
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
28 help="Image voxels with this intensity and below will be invisible."/>
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
29 <expand macro="params/intensity" name="end" value="0.5" label="Ramp end"
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
30 help="Image voxels with this intensity and above will have full visibility."/>
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
31 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
32 <when value="false"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
33 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
34 </xml>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
35 <xml name="when/builtin_cmap" tokens="value">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
36 <when value="@VALUE@">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
37 <expand macro="params/builtin_cmap"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
38 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
39 </xml>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
40 <xml name="test/params">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
41 <!-- CI tests use software rendering which requires very low sample rates -->
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
42 <param name="sample_rate_override" value="5"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
43 <param name="width" value="200"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
44 <param name="height" value="110"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
45 </xml>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
46 <xml name="test/assert_stdout">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
47 <assert_stdout>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
48 <has_line_matching expression="^EGL Vendor: .+"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
49 <yield/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
50 </assert_stdout>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
51 </xml>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
52 </macros>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
53 <creator>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
54 <expand macro="creators/bmcv"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
55 <expand macro="creators/kostrykin"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
56 </creator>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
57 <edam_operations>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
58 <edam_operation>operation_3443</edam_operation>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
59 </edam_operations>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
60 <xrefs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
61 <xref type="bio.tools">galaxy_image_analysis</xref>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
62 <xref type="bio.tools">giatools</xref>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
63 </xrefs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
64 <requirements>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
65 <!--
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
66 We employ here a custom Docker image until https://github.com/bioconda/bioconda-containers/issues/87 gets a better solution.
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
67
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
68 The Docker image is an extension of the BioContainer for the following packages:
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
69
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
70 <requirement type="package" version="@TOOL_VERSION@">libcarna-python</requirement>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
71 <requirement type="package" version="1.26.4">numpy</requirement>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
72 <requirement type="package" version="4.3.2">ffmpeg</requirement>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
73 <requirement type="package" version="0.7.3">giatools</requirement>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
74 <requirement type="package" version="0.12.2">ome-zarr</requirement>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
75 <requirement type="package" version="2.3.3">pandas</requirement>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
76
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
77 See https://github.com/kostrykin/LibCarna-Python-Docker for details of the image.
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
78 -->
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
79 <container type="docker">docker.io/kostrykin/libcarna-python:@TOOL_VERSION@-0</container>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
80 </requirements>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
81 <required_files>
3
31a2e1909ae5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065
imgteam
parents: 2
diff changeset
82 <include type="literal" path="render.py"/>
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
83 <exclude type="literal" path="README.md"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
84 </required_files>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
85 <command detect_errors="aggressive"><![CDATA[
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
86
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
87 python '$__tool_directory__/render.py'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
88
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
89 #if $intensities.extension == "zarr"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
90 --intensities '$intensities.extra_files_path/$intensities.metadata.store_root'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
91 #else
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
92 --intensities '$intensities'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
93 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
94
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
95 #if str($colormap.name) == "custom"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
96 --colormap '$colormap.custom'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
97 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
98
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
99 #if str($mask.enabled) == "true":
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
100 #if $mask.image.extension == "zarr"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
101 --mask '$mask.image.extra_files_path/$mask.image.metadata.store_root'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
102 #else
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
103 --mask '$mask.image'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
104 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
105 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
106
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
107 --html '$html'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
108 --params '$params'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
109 --verbose
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
110
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
111 ]]></command>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
112 <configfiles>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
113 <configfile name="params"><![CDATA[
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
114 {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
115
2
fe07197eb9a9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 05f00e4083f0593c15b5d2cfecd022302ae029aa
imgteam
parents: 1
diff changeset
116 #if int($sample_rate_override) > 0
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
117 #set $sample_rate = int($sample_rate_override)
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
118 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
119
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
120 "sample_rate": $sample_rate,
4
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
121 "units": "$units",
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
122 "axes": "$axes",
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
123 "width": $width,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
124 "height": $height,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
125 "mode": "$mode.name",
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
126
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
127 "mode_kwargs": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
128 #if str($mode.name) == "dvr"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
129 "translucency": $mode.translucency,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
130 "diffuse": $mode.diffuse
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
131 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
132 },
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
133
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
134 "colormap": "$colormap.name",
3
31a2e1909ae5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065
imgteam
parents: 2
diff changeset
135 "colorbar": $colorbar,
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
136
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
137 #if str($colormap.name) != "custom"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
138 "ramp": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
139 #if str($colormap.ramp.enabled) == "true"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
140 "start_type": "$colormap.ramp.start.type",
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
141 "start_value": $colormap.ramp.start.value,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
142 "end_type": "$colormap.ramp.end.type",
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
143 "end_value": $colormap.ramp.end.value
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
144 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
145 },
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
146 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
147
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
148 "camera": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
149 "distance": $camera.distance,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
150 "kwargs": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
151 "fov": $camera.fov,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
152 "z_near": $camera.z_near,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
153 "z_far": $camera.z_far
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
154 }
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
155 },
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
156 "video": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
157 "frames": $video.frames,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
158 "fps": $video.fps
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
159 },
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
160
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
161 "mask": $mask.enabled,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
162 "mask_renderer_kwargs": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
163 #if str($mask.enabled) == "true"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
164 "color": "$mask.color"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
165 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
166 }
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
167
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
168 }
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
169 ]]></configfile>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
170 </configfiles>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
171 <inputs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
172 <param name="intensities" type="data" format="tiff,zarr" label="Input image (3-D)">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
173 <expand macro="validators/is_single_channel"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
174 <expand macro="validators/is_single_frame"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
175 <expand macro="validators/is_3d"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
176 </param>
4
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
177 <param name="units" type="select" label="Unit of the intensity values">
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
178 <option value="raw" selected="true">No unit</option>
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
179 <option value="hu">Hounsfield</option>
a9f10dceb17e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 99d6ebe67515f1362ea4412b143ab2a140c8d631
imgteam
parents: 3
diff changeset
180 </param>
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
181 <param name="axes" type="select" label="Coordinate system">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
182 <option value="XZY" selected="true">Point Z to the top</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
183 <option value="XYZ">Point Y to the top</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
184 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
185 <param name="sample_rate" type="integer" min="100" value="800" label="Sample rate"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
186 help="Samples per pixel for volume rendering (ray marching)."/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
187 <param name="sample_rate_override" type="hidden" value="0"/><!-- For testing purposes -->
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
188 <param name="width" type="integer" min="50" max="1024" value="800" label="Width of the video (in pixels)"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
189 <param name="height" type="integer" min="50" max="1024" value="450" label="Height of the video (in pixels)"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
190 <conditional name="mode">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
191 <param name="name" type="select" label="Rendering mode">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
192 <option value="mip" selected="true">Maximum Intensity Projection (MIP)</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
193 <option value="dvr">Direct Volume Rendering (DVR)</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
194 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
195 <when value="mip"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
196 <when value="dvr">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
197 <param name="translucency" type="float" min="0" value="1" label="Translucency"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
198 <param name="diffuse" type="float" min="0" max="1" value="0.8" label="Directional light"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
199 help="Balances the amount of ambient vs directional light. The light is fully ambient for 0 and fully directional for 1."/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
200 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
201 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
202 <conditional name="colormap">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
203 <param name="name" type="select" label="Color map">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
204 <option value="custom">Custom</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
205 <expand macro="option/builtin_cmap_list"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
206 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
207 <when value="custom">
3
31a2e1909ae5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065
imgteam
parents: 2
diff changeset
208 <param name="custom" type="data" format="tabular" label="Custom color map">
31a2e1909ae5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065
imgteam
parents: 2
diff changeset
209 <validator type="dataset_metadata_in_range" metadata_name="columns" min="3" message="Color map needs to have at least 3 columns."/>
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
210 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
211 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
212 <expand macro="when/builtin_cmap_list"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
213 </conditional>
3
31a2e1909ae5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065
imgteam
parents: 2
diff changeset
214 <param name="colorbar" type="boolean" checked="true" label="Add a color bar"/>
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
215 <section name="camera" title="Camera parameters" expanded="true">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
216 <param name="fov" type="float" min="10" max="170" value="90" label="Field of view (in degrees)"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
217 <param name="distance" type="float" min="1" value="200" label="Distance"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
218 help="Distance between the camera and the center of the 3-D image."/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
219 <param name="z_near" type="float" min="0.01" value="10" label="Near clipping plane"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
220 help="Position of the near clipping plane along the z-axis."/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
221 <param name="z_far" type="float" min="100" value="1000" label="Far clipping plane"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
222 help="Position of the far clipping plane along the z-axis."/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
223 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
224 <conditional name="mask">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
225 <param name="enabled" type="select" label="Render mask overlay">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
226 <option value="false" selected="true">No overlay</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
227 <option value="true">Render mask overlay</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
228 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
229 <when value="false"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
230 <when value="true">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
231 <param name="image" type="data" format="tiff,zarr" label="Mask overlay (3-D)">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
232 <expand macro="validators/is_single_channel"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
233 <expand macro="validators/is_single_frame"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
234 <expand macro="validators/is_3d"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
235 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
236 <param name="color" type="color" value="#00ff00" label="Color of the overlay"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
237 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
238 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
239 <section name="video" title="Video parameters" expanded="false">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
240 <param name="frames" type="integer" min="10" value="200" label="Frames"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
241 <param name="fps" type="integer" min="1" max="60" value="25" label="Frames per second"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
242 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
243 </inputs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
244 <outputs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
245 <data format="html" name="html"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
246 </outputs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
247 <tests>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
248 <!-- Test with MIP -->
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
249 <test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
250 <param name="intensities" value="input/float32_10z_32y_40x.tiff"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
251 <section name="camera">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
252 <param name="distance" value="50"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
253 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
254 <output name="html" ftype="html" value="output/float32_10z_32y_40x-mip.html" compare="sim_size" delta="1000"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
255 <expand macro="test/params"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
256 <expand macro="test/assert_stdout"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
257 </test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
258 <!-- Test with DVR, ramp colormap, and mask -->
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
259 <test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
260 <param name="intensities" value="input/float32_10z_32y_40x.tiff"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
261 <conditional name="mode">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
262 <param name="name" value="dvr"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
263 <param name="translucency" value="0"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
264 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
265 <conditional name="colormap">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
266 <param name="name" value="BrBG"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
267 <conditional name="ramp">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
268 <param name="enabled" value="true"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
269 <section name="start">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
270 <param name="type" value="relative"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
271 <param name="value" value="0.33"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
272 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
273 <section name="end">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
274 <param name="type" value="relative"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
275 <param name="value" value="0.37"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
276 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
277 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
278 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
279 <section name="camera">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
280 <param name="distance" value="50"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
281 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
282 <conditional name="mask">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
283 <param name="enabled" value="true"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
284 <param name="image" value="input/uint8_10z_32y_40x.tiff"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
285 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
286 <output name="html" ftype="html" value="output/float32_10z_32y_40x-dvr-mask.html" compare="sim_size" delta="1000"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
287 <expand macro="test/params"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
288 <expand macro="test/assert_stdout"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
289 </test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
290 <!-- Test with custom colormap -->
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
291 <test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
292 <param name="intensities" value="input/float32_10z_32y_40x.tiff"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
293 <param name="axes" value="XYZ"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
294 <conditional name="colormap">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
295 <param name="name" value="custom"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
296 <param name="custom" value="input/colormap.tsv"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
297 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
298 <section name="camera">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
299 <param name="distance" value="50"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
300 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
301 <output name="html" ftype="html" value="output/float32_10z_32y_40x-colormap.html" compare="sim_size" delta="1000"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
302 <expand macro="test/params"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
303 <expand macro="test/assert_stdout"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
304 </test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
305 <!-- Test with Zarr and missing `z_spacing` metadata -->
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
306 <test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
307 <param name="intensities" value="input/float32_5z_16y_20x-no_z_spacing.zarr"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
308 <section name="camera">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
309 <param name="distance" value="50"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
310 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
311 <output name="html" ftype="html" value="output/float32_5z_16y_20x.html" compare="sim_size" delta="1000"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
312 <expand macro="test/params"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
313 <expand macro="test/assert_stdout"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
314 </test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
315 </tests>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
316 <help>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
317
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
318 **Renders videos for visualization of 3-D image data.**
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
319
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
320 The image data is rotated to facilitate grasping visual information from different angles.
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
321
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
322 LibCarna employs a volume rendering technique called *ray marching* and permits different visualization modes, including *maximum intensity projections* (MIP) and *direct volume rendering* (DVR). In addition, the renderings can be augmented with binary or label masks (e.g., segmentation overlays).
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
323
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
324 .. image:: dvr.gif
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
325 :width: 438px
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
326 :scale: 100%
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
327
3
31a2e1909ae5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065
imgteam
parents: 2
diff changeset
328 An overview of the available color maps is available at `matplotlib.org`_.
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
329
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
330 .. _matplotlib.org: https://matplotlib.org/stable/users/explain/colors/colormaps.html
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
331
3
31a2e1909ae5 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 9abf60fee6ba4f5d4f4a18d8f4d33e6263b3c065
imgteam
parents: 2
diff changeset
332 When using custom color maps, a tabular file with at least 3 columns must be used (`intensity`, `type`, `color`). Each pair of consecutive rows defines a linear segment of the color map. The `intensity` values can be given either as absolute intensity values, or as relative values where 0 and 1 correspond to the minimum and maximum intensities of the image data, respectively. The `type` column indicates whether the corresponding `intensity` value is `absolute` or `relative`. The `color` must be given in hexadecimal notation with a ``#`` prefix and must be either 6 or 8 digits long (6 for RGB and 8 for RGBA). An example is given below.
0
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
333
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
334 +-----------+------------+----------+
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
335 | color | intensity | type |
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
336 +-----------+------------+----------+
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
337 | #ff00007f | 0 | absolute |
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
338 +-----------+------------+----------+
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
339 | #ffff00ff | 0.5 | absolute |
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
340 +-----------+------------+----------+
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
341 | #00ffffff | 1.0 | relative |
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
342 +-----------+------------+----------+
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
343
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
344 </help>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
345 <citations>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
346 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
347 </citations>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
348 </tool>