Mercurial > repos > imgteam > mahotas_features

annotate mahotas_features.xml @ 1:3aaf74f7515a 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/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:22:36 +0000
parents de5c698b251c
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
1 <tool id="ip_mahotas_features" name="Compute image features" version="0.7-2">
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
2 <description>with Mahotas</description>
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
3 <edam_operations>
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
4 <edam_operation>operation_3443</edam_operation>
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
5 </edam_operations>
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
6 <xrefs>
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
7 <xref type="biii">mahotas-feature-computation</xref>
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
8 </xrefs>
0
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
9 <requirements>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
10 <requirement type="package" version="1.4.3">mahotas</requirement>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
11 <requirement type="package" version="4.0.0">pillow</requirement>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
12 <requirement type="package" version="1.12">numpy</requirement>
1
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
13 <requirement type="package" version="0.15.1">tifffile</requirement>
0
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
14 </requirements>
1
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
15 <command detect_errors="aggressive"><![CDATA[
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
16 /usr/local/bin/mahotas-features.py
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
17 #set files = '" "'.join( [ str( $file ) for $file in $inputs ] )
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
18 "${files}"
0
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
19
1
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
20 --output $output
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
21 --convert-to-bw $convertbw
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
22 $haralick
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
23 $lbp
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
24 --clobber
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
25 #if $lbpradius and $lbpradius is not None:
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
26 --lbp-radius $lbpradius
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
27 #end if
0
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
28
1
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
29 #if $lbppoints and $lbppoints is not None:
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
30 --lbp-points $lbppoints
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
31 #end if]]>
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
32 </command>
0
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
33 <inputs>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
34 <param name="inputs" type="data" format="tiff,png,jpg,bmp" multiple="True" label="Image files"/>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
35 <param name="convertbw" type="select" label="Convert color images to greyscale">
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
36 <option value="no" selected="True">no</option>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
37 <option value="max">max projection</option>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
38 <option value="yes">yes</option>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
39 </param>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
40 <param checked="true" help="(--haralick)" label="Compute Haralick features" name="haralick" type="boolean" truevalue="--haralick" falsevalue=""/>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
41 <param checked="true" help="(--lbp)" label="Compute LBP (linear binary patterns) features" name="lbp" type="boolean" truevalue="--lbp" falsevalue=""/>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
42 <param help="(--lbp-radius)" label="Radius to use for LBP features" name="lbpradius" optional="true" type="integer" value="8"/>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
43 <param help="(--lbp-points)" label="Nr of points to use for LBP features" name="lbppoints" optional="true" type="integer" value="6"/>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
44 </inputs>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
45 <outputs>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
46 <data format="tsv" hidden="false" name="output"/>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
47 </outputs>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
48 <tests>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
49 <test>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
50 <param name="inputs" value="galaxyIcon_noText.png"/>
1
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
51 <param name="haralick" value="true"/>
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
52 <param name="lbp" value="true"/>
3aaf74f7515a planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/mahotas-features/ commit 8e99ddb62ceab1da15996906a0813826b62d38fe
imgteam
parents: 0
diff changeset
53 <param name="convertbw" value="max"/>
0
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
54 <output name="output" file="features.tsv" ftype="tsv" lines_diff="2"/>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
55 </test>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
56 </tests>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
57 <help>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
58 **What it does**
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
59
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
60 Mahotas is a computer vision and image processing library for Python. This tools computes features using mahotas.
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
61 </help>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
62 <citations>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
63 <citation type="doi">10.5334/jors.ac</citation>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
64 </citations>
de5c698b251c planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/mahotas-features/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
imgteam
parents:
diff changeset
65 </tool>