Mercurial > repos > imgteam > scale_image

annotate scale_image.xml @ 3:d09507d3fb0e 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/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
author imgteam
date Fri, 10 Nov 2023 14:23:33 +0000
parents f3c05a734dd1
children 3179853faae9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
3
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
1 <tool id="ip_scale_image" name="Scale image" version="0.4-2">
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
2 <description>with scikit-image</description>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
3 <edam_operations>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
4 <edam_operation>operation_3443</edam_operation>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
5 </edam_operations>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
6 <xrefs>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
7 <xref type="bio.tools">scikit-image</xref>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
8 <xref type="biii">scikit-image</xref>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
9 </xrefs>
0
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
10 <requirements>
2
f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 1
diff changeset
11 <requirement type="package" version="6.1.0">pillow</requirement>
0
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
12 <requirement type="package" version="0.14.2">scikit-image</requirement>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
13 <requirement type="package" version="1.15.4">numpy</requirement>
2
f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 1
diff changeset
14 <requirement type="package" version="1.1.0">scipy</requirement>
f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 1
diff changeset
15 <requirement type="package" version="0.15.1">tifffile</requirement>
f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 1
diff changeset
16 </requirements>
f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
parents: 1
diff changeset
17 <command detect_errors="aggressive">
0
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
18 <![CDATA[
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
19 python '$__tool_directory__/scale_image.py' '$input' ./out.png
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
20 #if $use_scale_option.use_scale == 'true'
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
21 $use_scale_option.scale
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
22 #else if $use_scale_option.use_scale == 'false'
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
23 '[$use_scale_option.scale_x, $use_scale_option.scale_y]'
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
24 #end if
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
25 $order
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
26
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
27 ]]>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
28 </command>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
29 <inputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
30 <param name="input" type="data" format="png" label="Image file"/>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
31 <conditional name="use_scale_option"><!--a third option (using one integer as percentage scaling) could still be implemented-->
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
32 <param label="Lock scaling between image dimensions" name="use_scale" type="select">
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
33 <option selected="true" value="true">Lock</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
34 <option value="false">Individual scales</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
35 </param>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
36 <when value="true">
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
37 <param name="scale" type="float" value="1.0" label="Scaling factor" />
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
38 </when>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
39 <when value="false">
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
40 <param name="scale_x" type="integer" value="100" label="New height of the image in pixels" />
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
41 <param name="scale_y" type="integer" value="100" label="New width of the image in pixels" />
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
42 </when>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
43 </conditional>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
44 <param name="order" type="select" label="Interpolation method">
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
45 <option value="0">Nearest-neighbor</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
46 <option value="1" selected="true">Bi-linear</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
47 <option value="2">Bi-cubic</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
48 </param>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
49 </inputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
50 <outputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
51 <data format="png" name="output" from_work_dir="out.png"/>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
52 </outputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
53 <tests>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
54 <test>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
55 <param name="input" value="sample1.png"/> <!--continue here-->
3
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
56 <conditional name="use_scale_option">
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
57 <param name="use_scale" value="false"/>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
58 <param name="scale_x" value="200"/>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
59 <param name="scale_y" value="150"/>
d09507d3fb0e planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/scale_image/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d
imgteam
parents: 2
diff changeset
60 </conditional>
0
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
61 <param name="order" value="0"/>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
62 <output name="output" value="out2.png" ftype="png" compare="sim_size"/>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
63 </test>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
64 </tests>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
65 <help>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
66 **What it does**
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
67
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
68 This tool scales an image using the scaling factor.
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
69 </help>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
70 <citations>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
71 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
72 </citations>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
73 </tool>