Mercurial > repos > imgteam > split_image

annotate split_image.xml @ 2:227e8928af6e 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/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
author imgteam
date Fri, 12 Dec 2025 21:02:25 +0000
parents 4b7940d0c051
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
1 <tool id="ip_split_image" name="Split image along axes" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
2 <description>with NumPy</description>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
3 <macros>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
4 <import>creators.xml</import>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
5 <import>tests.xml</import>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
6 <token name="@TOOL_VERSION@">2.3.5</token>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
7 <token name="@VERSION_SUFFIX@">0</token>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
8 </macros>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
9 <creator>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
10 <expand macro="creators/bmcv"/>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
11 <expand macro="creators/kostrykin"/>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
12 </creator>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
13 <edam_operations>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
14 <edam_operation>operation_3443</edam_operation>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
15 </edam_operations>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
16 <xrefs>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
17 <xref type="bio.tools">galaxy_image_analysis</xref>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
18 </xrefs>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
19 <requirements>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
20 <requirement type="package" version="@TOOL_VERSION@">numpy</requirement>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
21 <requirement type="package" version="0.5.2">giatools</requirement>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
22 <requirement type="package" version="2025.10.16">tifffile</requirement>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
23 </requirements>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
24 <command detect_errors="aggressive"><![CDATA[
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
25
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
26 mkdir output &&
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
27 python '$__tool_directory__/split.py'
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
28
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
29 '$input'
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
30 '$axis'
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
31 output
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
32
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
33 $squeeze
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
34
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
35 ]]></command>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
36 <inputs>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
37 <param name="input" type="data" format="tiff,png" label="Image to split" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
38 <param name="axis" type="select" label="Axis to split along">
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
39 <option value="T">T-axis (split the frames of a temporal image sequence)</option>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
40 <option value="Z">Z-axis (split the slices of a 3-D image or image sequence)</option>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
41 <option value="C" selected="true">C-axis (split the channels of an image or image sequence)</option>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
42 <option value="S">S-axis (split the samples of an image or image sequence)</option>
1
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
43 <option value="Q">Q-axis (other or unknown axis)</option>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
44 <option value="">Split dataset that contains multiple images (e.g., multi-series TIFF)</option>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
45 </param>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
46 <param name="squeeze" type="boolean" checked="false" truevalue="--squeeze" falsevalue="" label="Squeeze result images"
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
47 help="Only non-singleton axes (axes with more than one element) will be retained in the result images. This does not apply for the X and Y axes which always are retained." />
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
48 </inputs>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
49 <outputs>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
50 <collection type="list" name="output" label="Split ${on_string} along ${axis} axis">
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
51 <discover_datasets directory="output" pattern="__name__" format="tiff" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
52 </collection>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
53 </outputs>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
54 <tests>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
55
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
56 <!-- PNG tests -->
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
57 <test>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
58 <param name="input" value="rgb1.png" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
59 <param name="axis" value="C" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
60 <param name="squeeze" value="false" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
61 <output_collection name="output" type="list" count="3">
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
62 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_r.tiff" ftype="tiff"/>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
63 <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_g.tiff" ftype="tiff"/>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
64 <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_b.tiff" ftype="tiff"/>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
65 </output_collection>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
66 <assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
67 <has_line line="Input image axes: YXC"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
68 <has_line line="Input image shape: (32, 32, 3)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
69 <has_line line="Writing 3 image(s)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
70 <has_line line="Output axes: YXC"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
71 <has_line line="Output shape: (32, 32, 1)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
72 </assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
73 </test>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
74 <test>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
75 <param name="input" value="rgb1.png" />
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
76 <param name="axis" value="" />
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
77 <param name="squeeze" value="false" />
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
78 <output_collection name="output" type="list" count="1">
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
79 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1.tiff" ftype="tiff"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
80 </output_collection>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
81 <assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
82 <has_line line="Not a TIFF file"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
83 <has_line line="Writing 1 image(s)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
84 <has_line line="Output axes: YXC"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
85 <has_line line="Output shape: (32, 32, 3)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
86 </assert_stdout>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
87 </test>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
88
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
89 <!-- TIFF tests -->
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
90 <test>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
91 <param name="input" value="zcyx.tiff" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
92 <param name="axis" value="Z" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
93 <param name="squeeze" value="false" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
94 <output_collection name="output" type="list" count="25">
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
95 <expand macro="tests/intensity_image_diff/element" name="01.tiff" value="zcyx_slice01.tiff" ftype="tiff"/>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
96 <expand macro="tests/intensity_image_diff/element" name="25.tiff" value="zcyx_slice25.tiff" ftype="tiff"/>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
97 </output_collection>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
98 <assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
99 <has_line line="Input image axes: ZCYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
100 <has_line line="Input image shape: (25, 2, 50, 50)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
101 <has_line line="Writing 25 image(s)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
102 <has_line line="Output axes: ZCYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
103 <has_line line="Output shape: (1, 2, 50, 50)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
104 </assert_stdout>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
105 </test>
1
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
106 <test>
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
107 <param name="input" value="qyx.tiff" />
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
108 <param name="axis" value="Q" />
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
109 <param name="squeeze" value="false" />
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
110 <output_collection name="output" type="list" count="2">
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
111 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx_q1.tiff" ftype="tiff"/>
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
112 <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="qyx_q2.tiff" ftype="tiff"/>
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
113 </output_collection>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
114 <assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
115 <has_line line="Input image axes: QYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
116 <has_line line="Input image shape: (2, 256, 256)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
117 <has_line line="Writing 2 image(s)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
118 <has_line line="Output axes: QYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
119 <has_line line="Output shape: (1, 256, 256)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
120 </assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
121 </test>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
122 <test>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
123 <param name="input" value="qyx.tiff" />
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
124 <param name="axis" value="" />
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
125 <param name="squeeze" value="false" />
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
126 <output_collection name="output" type="list" count="1">
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
127 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="qyx.tiff" ftype="tiff"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
128 </output_collection>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
129 <assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
130 <has_line line="Found TIFF with 1 series"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
131 </assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
132 </test>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
133
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
134 <!-- Test splitting multi-series TIFF -->
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
135 <test>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
136 <param name="input" value="multiseries.ome.tiff" />
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
137 <param name="axis" value="" />
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
138 <param name="squeeze" value="false" />
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
139 <output_collection name="output" type="list" count="6">
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
140 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="multiseries_series1.tiff" ftype="tiff"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
141 <expand macro="tests/intensity_image_diff/element" name="6.tiff" value="multiseries_series6.tiff" ftype="tiff"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
142 </output_collection>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
143 <assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
144 <has_line line="Found TIFF with 6 series"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
145 <has_line line="Writing 6 image(s)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
146 <has_line line="Output 1 axes: CYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
147 <has_line line="Output 1 shape: (4, 5, 5)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
148 <has_line line="Output 2 axes: CYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
149 <has_line line="Output 2 shape: (4, 5, 5)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
150 <has_line line="Output 3 axes: CYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
151 <has_line line="Output 3 shape: (4, 5, 5)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
152 <has_line line="Output 4 axes: CYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
153 <has_line line="Output 4 shape: (4, 5, 5)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
154 <has_line line="Output 5 axes: CYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
155 <has_line line="Output 5 shape: (4, 5, 5)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
156 <has_line line="Output 6 axes: CYX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
157 <has_line line="Output 6 shape: (4, 5, 5)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
158 </assert_stdout>
1
4b7940d0c051 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 6152e9fafda27f76c1e96e533143f86fe605e2da
imgteam
parents: 0
diff changeset
159 </test>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
160
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
161 <!-- Test squeezing -->
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
162 <test>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
163 <param name="input" value="rgb1.png" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
164 <param name="axis" value="C" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
165 <param name="squeeze" value="true" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
166 <output_collection name="output" type="list" count="3">
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
167 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_squeezed_r.tiff" ftype="tiff"/>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
168 <expand macro="tests/intensity_image_diff/element" name="2.tiff" value="rgb1_squeezed_g.tiff" ftype="tiff"/>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
169 <expand macro="tests/intensity_image_diff/element" name="3.tiff" value="rgb1_squeezed_b.tiff" ftype="tiff"/>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
170 </output_collection>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
171 <assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
172 <has_line line="Input image axes: YXC"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
173 <has_line line="Input image shape: (32, 32, 3)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
174 <has_line line="Writing 3 image(s)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
175 <has_line line="Output axes: YX"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
176 <has_line line="Output shape: (32, 32)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
177 </assert_stdout>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
178 </test>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
179
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
180 <!-- Test with missing axes -->
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
181 <test>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
182 <param name="input" value="rgb1.png" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
183 <param name="axis" value="Z" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
184 <param name="squeeze" value="false" />
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
185 <output_collection name="output" type="list" count="1">
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
186 <expand macro="tests/intensity_image_diff/element" name="1.tiff" value="rgb1_split_z.tiff" ftype="tiff"/>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
187 </output_collection>
2
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
188 <assert_stdout>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
189 <has_line line="Input image axes: YXC"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
190 <has_line line="Input image shape: (32, 32, 3)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
191 <has_line line="Writing 1 image(s)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
192 <has_line line="Output axes: YXC"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
193 <has_line line="Output shape: (32, 32, 3)"/>
227e8928af6e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit 5e452f10eb88f0fa8a420eec66c6c97e3060e433
imgteam
parents: 1
diff changeset
194 </assert_stdout>
0
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
195 </test>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
196
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
197 </tests>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
198 <help>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
199
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
200 **Splits an image along a specific axis (e.g., channels).**
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
201
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
202 This tool splits an image along a specifc axis and yields a collection of images.
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
203 This can be used, for example, to convert a multi-channel image into a collection of single-channel images.
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
204
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
205 The pixel data type of the split image is preserved (will be the same as the input image).
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
206
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
207 </help>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
208 <citations>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
209 <citation type="doi">10.1038/s41586-020-2649-2</citation>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
210 </citations>
5deaa390ca62 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/split_image/ commit f1052360d410594fa1795cf0e02576b8fa4d4135
imgteam
parents:
diff changeset
211 </tool>