Mercurial > repos > imgteam > points2binaryimage

annotate points2binaryimage.xml @ 3:a80f92ec6f89 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/points2binaryimage/ commit 2994366afa0a1c537c0edf6c4578bda079494b2f
author imgteam
date Wed, 26 Jun 2024 08:35:56 +0000
parents 2ad6350df85b
children 4c0f16fb9f8d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
1 <tool id="ip_points_to_binaryimage" name="Convert point coordinates to binary image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
1
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
2 <description></description>
2
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
3 <macros>
3
a80f92ec6f89 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2994366afa0a1c537c0edf6c4578bda079494b2f
imgteam
parents: 2
diff changeset
4 <import>creators.xml</import>
2
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
5 <token name="@TOOL_VERSION@">0.2</token>
3
a80f92ec6f89 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2994366afa0a1c537c0edf6c4578bda079494b2f
imgteam
parents: 2
diff changeset
6 <token name="@VERSION_SUFFIX@">3</token>
2
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
7 </macros>
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
8 <creator>
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
9 <expand macro="creators/bmcv" />
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
10 </creator>
1
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
11 <edam_operations>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
12 <edam_operation>operation_3443</edam_operation>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
13 </edam_operations>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
14 <xrefs>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
15 <xref type="bio.tools">galaxy_image_analysis</xref>
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
16 </xrefs>
0
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
17 <requirements>
1
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
18 <requirement type="package" version="0.14.2">scikit-image</requirement>
0
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
19 <requirement type="package" version="1.15.4">numpy</requirement>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
20 <requirement type="package" version="0.23.4">pandas</requirement>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
21 <requirement type="package" version="2018.7">pytz</requirement><!--pandas seems to have additional requirements that are not automatically installed-->
2
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
22 <requirement type="package" version="2.5.2">python-dateutil</requirement>
1
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
23 <requirement type="package" version="0.15.1">tifffile</requirement>
0
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
24 </requirements>
1
90385ec28b34 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf
imgteam
parents: 0
diff changeset
25 <command detect_errors="aggressive">
0
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
26 <![CDATA[
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
27 python '$__tool_directory__/points2binaryimage.py' '$input' '$output' $shapex $shapey $has_header $invert_xy
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
28 ]]>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
29 </command>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
30 <inputs>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
31 <param name="input" type="data" format="tabular" label="CSV point file"/>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
32 <param name="shapex" type="integer" value="500" optional="true" min="1" max="2000" label="Width of output image" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
33 <param name="shapey" type="integer" value="500" optional="true" min="1" max="2000" label="Height of output image" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
34 <param name="has_header" type="boolean" checked="false" truevalue="--has_header True" falsevalue="" optional="true" label="Does point file contain header?" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
35 <param name="invert_xy" type="boolean" checked="false" falsevalue="" truevalue="--invert_xy True" optional="true" label="Inverts x and y in CSV point file" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
36 </inputs>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
37 <outputs>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
38 <data name="output" format="tiff" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
39 </outputs>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
40 <tests>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
41 <test>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
42 <param name="input" value="points.tsv" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
43 <param name="shapex" value="20" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
44 <param name="shapey" value="30" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
45 <param name="has_header" value="false" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
46 <param name="invert_xy" value="true" />
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
47 <output name="output" ftype="tiff" file="out.tiff" compare="sim_size"/>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
48 </test>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
49 </tests>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
50 <help>
2
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
51
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
52 This tool converts a CSV list of points to a binary image by rasterizing the point coordinates.
0
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
53
2
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
54 The created image is a single-channel image with 16 bits per pixel (unsigned integer).
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
55 The points are rasterized with value 32767 (white).
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
56 Pixels not corresponding to any points in the CSV are assigned the value 0 (black).
2ad6350df85b planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2binaryimage/ commit 7830f8c03f6ac044b67fb7999a91c574a11c7d2c
imgteam
parents: 1
diff changeset
57
0
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
58 </help>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
59 <citations>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
60 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
61 </citations>
dd513c9f5230 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/points2binaryimage/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
62 </tool>