Mercurial > repos > imgteam > slice_image

annotate slice_image.xml @ 2:f312d414f234 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/slice_image/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
author imgteam
date Mon, 13 Nov 2023 22:12:22 +0000
parents 8856a7c85e4c
children 1faa7e3c94ff
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
f312d414f234 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
1 <tool id="ip_slice_image" name="Slice image" version="0.3-2">
f312d414f234 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
2 <description></description>
f312d414f234 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
3 <edam_operations>
f312d414f234 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
4 <edam_operation>operation_3443</edam_operation>
f312d414f234 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
5 </edam_operations>
f312d414f234 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
6 <xrefs>
f312d414f234 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
7 <xref type="bio.tools">galaxy_image_analysis</xref>
f312d414f234 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/slice_image/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 1
diff changeset
8 </xrefs>
0
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
9 <requirements>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
10 <requirement type="package" version="0.14.2">scikit-image</requirement>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
11 <requirement type="package" version="1.15.4">numpy</requirement>
1
8856a7c85e4c "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 0
diff changeset
12 <requirement type="package" version="1.1.0">scipy</requirement>
8856a7c85e4c "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 0
diff changeset
13 <requirement type="package" version="0.15.1">tifffile</requirement>
0
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
14 </requirements>
1
8856a7c85e4c "planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit 3d389fdec0db29cf6fbd783c0501455bf624fa90"
imgteam
parents: 0
diff changeset
15 <command detect_errors="aggressive">
0
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
16 <![CDATA[
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
17 mkdir ./out &&
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
18 python '$__tool_directory__/slice_image.py'
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
19 '$input_file' ./out
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
20 --stride $stride --window_size $patch_size --bg_thresh $bg_thresh
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
21 --limit_slices $limit_slices
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
22 #if $limit_slices:
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
23 --n_thresh $n_thresh
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
24 #end if
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
25 #if $control_rng:
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
26 --seed $seed
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
27 #end if
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
28 && ls -l ./out
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
29 ]]>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
30 </command>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
31 <inputs>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
32 <param name="input_file" type="data" format="tiff,png,jpg,bmp" label="Input image"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
33 <!--<param name="out_folder" type="text" label="Output folder for image slices"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
34 <param name="label_file" type="data" format="tiff,png,jpg,bmp" label="Auxiliary label file to split in the same way"/>-->
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
35 <param name="stride" type="integer" optional="true" value="16"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
36 <param name="patch_size" type="integer" optional="true" value="64" label="Size of resulting (quadratic-shaped) slices"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
37 <param name="bg_thresh" type="float" optional="true" value="0" label="Threshold to not be considered background"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
38 <param name="limit_slices" type="boolean" checked="true" label="Should the number of slices be limited?"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
39 <param name="n_thresh" type="integer" optional="true" label="Maximum amount of slices; only needed if limit_slices is selected"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
40 <param name="control_rng" type="boolean" checked="false" label="Boolean that controls if a certain seed should be selected for the random number generator"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
41 <param name="seed" type="integer" value="1"
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
42 label="Seed chosen for the random number generator of the random choice of limited slices. Only required if cotrol_rng is selected"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
43 </inputs>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
44 <outputs>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
45 <collection name="slices" type="list" label="Slices obtained from input">
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
46 <discover_datasets directory="out" format="tiff" pattern="__name__"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
47 </collection>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
48 </outputs>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
49 <tests>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
50 <test>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
51 <param name="input_file" value="input.tiff"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
52 <param name="limit_slices" value="true"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
53 <param name="n_thresh" value="5"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
54 <param name="control_rng" value="true"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
55 <param name="seed" value="17"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
56 <output_collection name="slices" type="list">
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
57 <element name="148.tiff" file="input_148.tiff" ftype="tiff" compare="sim_size"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
58 <element name="155.tiff" file="input_155.tiff" ftype="tiff" compare="sim_size"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
59 <element name="187.tiff" file="input_187.tiff" ftype="tiff" compare="sim_size"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
60 <element name="212.tiff" file="input_212.tiff" ftype="tiff" compare="sim_size"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
61 <element name="267.tiff" file="input_267.tiff" ftype="tiff" compare="sim_size"/>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
62 </output_collection>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
63 </test>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
64 </tests>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
65 <help>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
66 **What it does**
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
67
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
68 Slices image into multiple smaller patches.
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
69 </help>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
70 <citations>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
71 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
72 </citations>
aacfbd7c4af6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/slice_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
73 </tool>