Mercurial > repos > imgteam > libcarna_render

annotate render.xml @ 0:7d6be2b7e1e2 draft

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 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
author imgteam
date Mon, 05 Jan 2026 20:10:28 +0000
parents
children 22618ff03b3d
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>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
8 <token name="@VERSION_SUFFIX@">0</token>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
9 <xml name="params/intensity" tokens="name,label">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
10 <section name="@NAME@" title="@LABEL@" expanded="true">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
11 <param name="type" type="select" label="@LABEL@"
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.">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
13 <option value="absolute" selected="true">Absolute intensity value</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
14 <option value="relative">Relative intensity value</option>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
15 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
16 <param name="value" type="float" label="Intensity value"/>
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"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
22 help="Use a piecewise linear ramp function for the alpha channel of the colormap.">
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">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
27 <expand macro="params/intensity" name="start" label="Ramp start"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
28 <expand macro="params/intensity" name="end" label="Ramp end"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
29 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
30 <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
31 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
32 </xml>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
33 <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
34 <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
35 <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
36 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
37 </xml>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
38 <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
39 <!-- 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
40 <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
41 <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
42 <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
43 </xml>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
44 <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
45 <assert_stdout>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
46 <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
47 <yield/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
48 </assert_stdout>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
49 </xml>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
50 </macros>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
51 <creator>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
52 <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
53 <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
54 </creator>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
55 <edam_operations>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
56 <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
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 <xrefs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
59 <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
60 <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
61 </xrefs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
62 <requirements>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
63 <!--
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
64 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
65
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
66 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
67
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
68 <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
69 <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
70 <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
71 <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
72 <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
73 <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
74
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
75 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
76 -->
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
77 <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
78 </requirements>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
79 <required_files>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
80 <include type="literal" path="clip_image.py"/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
81 <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
82 </required_files>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
83 <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
84
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
85 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
86
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
87 #if $intensities.extension == "zarr"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
88 --intensities '$intensities.extra_files_path/$intensities.metadata.store_root'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
89 #else
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
90 --intensities '$intensities'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
91 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
92
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
93 #if str($colormap.name) == "custom"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
94 --colormap '$colormap.custom'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
95 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
96
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
97 #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
98 #if $mask.image.extension == "zarr"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
99 --mask '$mask.image.extra_files_path/$mask.image.metadata.store_root'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
100 #else
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
101 --mask '$mask.image'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
102 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
103 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
104
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
105 --html '$html'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
106 --params '$params'
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
107 --verbose
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
108
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
109 ]]></command>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
110 <configfiles>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
111 <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
112 {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
113
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
114 #if str($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
115 #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
116 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
117
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
118 "sample_rate": $sample_rate,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
119 "axes": "$axes",
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
120 "width": $width,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
121 "height": $height,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
122 "mode": "$mode.name",
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
123
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
124 "mode_kwargs": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
125 #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
126 "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
127 "diffuse": $mode.diffuse
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
128 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
129 },
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
130
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
131 "colormap": "$colormap.name",
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 #if str($colormap.name) != "custom"
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
134 "ramp": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
135 #if str($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
136 "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
137 "start_value": $colormap.ramp.start.value,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
138 "end_type": "$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
139 "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
140 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
141 },
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
142 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
143
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
144 "camera": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
145 "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
146 "kwargs": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
147 "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
148 "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
149 "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
150 }
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
151 },
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
152 "video": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
153 "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
154 "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
155 },
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
156
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
157 "mask": $mask.enabled,
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
158 "mask_renderer_kwargs": {
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
159 #if str($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
160 "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
161 #end if
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
162 }
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
163
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
164 }
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
165 ]]></configfile>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
166 </configfiles>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
167 <inputs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
168 <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
169 <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
170 <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
171 <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
172 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
173 <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
174 <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
175 <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
176 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
177 <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
178 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
179 <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
180 <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
181 <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
182 <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
183 <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
184 <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
185 <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
186 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
187 <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
188 <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
189 <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
190 <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
191 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
192 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
193 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
194 <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
195 <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
196 <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
197 <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
198 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
199 <when value="custom">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
200 <param name="custom" type="data" format="tabular" label="Custom colormap">
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
201 <validator type="dataset_metadata_in_range" metadata_name="columns" min="3" message="Colormap needs to have at least 3 columns."/>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
202 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
203 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
204 <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
205 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
206 <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
207 <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
208 <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
209 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
210 <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
211 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
212 <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
213 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
214 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
215 <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
216 <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
217 <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
218 <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
219 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
220 <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
221 <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
222 <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
223 <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
224 <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
225 <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
226 </param>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
227 <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
228 </when>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
229 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
230 <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
231 <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
232 <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
233 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
234 </inputs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
235 <outputs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
236 <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
237 </outputs>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
238 <tests>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
239 <!-- 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
240 <test>
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="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
242 <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
243 <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
244 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
245 <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
246 <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
247 <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
248 </test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
249 <!-- 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
250 <test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
251 <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
252 <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
253 <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
254 <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
255 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
256 <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
257 <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
258 <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
259 <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
260 <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
261 <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
262 <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
263 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
264 <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
265 <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
266 <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
267 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
268 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
269 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
270 <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
271 <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
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 <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
274 <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
275 <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
276 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
277 <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
278 <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
279 <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
280 </test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
281 <!-- 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
282 <test>
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="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
284 <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
285 <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
286 <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
287 <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
288 </conditional>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
289 <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
290 <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
291 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
292 <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
293 <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
294 <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
295 </test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
296 <!-- 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
297 <test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
298 <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
299 <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
300 <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
301 </section>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
302 <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
303 <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
304 <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
305 </test>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
306 </tests>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
307 <help>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
308
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
309 **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
310
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
311 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
312
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
313 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
314
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
315 .. 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
316 :width: 438px
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
317 :scale: 100%
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
318
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
319 An overview of the available colormaps is available at `matplotlib.org`_.
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
320
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
321 .. _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
322
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
323 When using custom colormaps, 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 colormap. 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.
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
324
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
325 +-----------+------------+----------+
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
326 | 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
327 +-----------+------------+----------+
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
328 | #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
329 +-----------+------------+----------+
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
330 | #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
331 +-----------+------------+----------+
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
332 | #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
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 </help>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
336 <citations>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
337 <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
338 </citations>
7d6be2b7e1e2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/libcarna/ commit 20db59ffe2a97f25d82ba02e451bf73f93ef84ee
imgteam
parents:
diff changeset
339 </tool>