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comparison bf2raw.xml @ 0:31fee86b0b75 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:22:22 +0000
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-1:000000000000 0:31fee86b0b75
1 <tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>with Bioformats</description>
3 <macros>
4 <import>creators.xml</import>
5 <token name="@TOOL_VERSION@">0.7.0</token>
6 <token name="@VERSION_SUFFIX@">3</token>
7 </macros>
8 <creator>
9 <expand macro="creators/bugraoezdemir"/>
10 </creator>
11 <edam_operations>
12 <edam_operation>operation_3443</edam_operation>
13 </edam_operations>
14 <requirements>
15 <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container>
16 </requirements>
17 <command><![CDATA[
18 if [ ! -d $output.files_path ];then
19 mkdir -p $output.files_path;
20 fi;
21
22 #if str($io_options.input.ext)=='html':
23 #set dirlist=os.listdir($io_options.input.files_path)
24 #assert len($dirlist) > 0
25 #set input_path=os.path.join(str($io_options.input.files_path), str($dirlist[0]))
26 #else:
27 #set input_path=$io_options.input
28 #end if
29
30 export _JAVA_OPTIONS="-Djava.io.tmpdir=/usr/local/man/" && bioformats2raw $input_path $output.files_path/$io_options.output_name
31 #if $bf2raw_params.multiscales['options'] == 'auto':
32 --target-min-size $bf2raw_params.multiscales.min_xy_size
33 #elif $bf2raw_params.multiscales['options'] == 'manual':
34 --resolutions $bf2raw_params.resolutions
35 #end if
36 --tile_height $bf2raw_params.tile_height
37 --tile_width $bf2raw_params.tile_width
38 --chunk_depth $bf2raw_params.chunk_depth
39 --downsample-type $bf2raw_params.downsample_type
40 --compression $bf2raw_params.compression
41 --max_workers "\${GALAXY_SLOTS:-4}"
42 $bf2raw_params.nesting
43 $bf2raw_params.omefolder
44 $bf2raw_params.droptop
45 #if not str($bf2raw_params.dimension_order) == 'keep input order':
46 --dimension-order $bf2raw_params.dimension_order
47 #end if
48 --overwrite &> /dev/null;
49
50 ]]></command>
51 <inputs>
52 <section name="io_options" title="Input-output paths" expanded="true">
53 <param name="input" type="data" format="scn,ndpi,tf8,vms,xml,pcx,binary,hdr,mov,psd,pbm,nrrd,tiff,pgm,ppm,txt,tf2,zip,top,gif,wav,btf,bmp,png,gz,cif,fli,btf,jpg,avi,html,sif,csv,ome.tiff,par,fits,jp2,eps,nhdr,svs,mrc" label="Input image located in Galaxy history"/>
54 <param name="output_name" type="text" value="output.ome.zarr" label="Name of the generated OME-Zarr"/>
55 </section>
56 <section name="bf2raw_params" title="Parameters fed to file conversion module">
57 <conditional name="multiscales" >
58 <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" >
59 <option value="auto" selected="true">auto</option>
60 <option value="manual" selected="false">manual</option>
61 </param>
62 <when value="auto">
63 <param name="min_xy_size" type="integer" min="1" optional="true" label="Min x-y dimension for the lowest resolution" value="256" />
64 </when>
65 <when value="manual">
66 <param name="resolution_count" type="integer" min="1" optional="true" label="Number of resolution layers" value="3"/>
67 </when>
68 </conditional >
69 <param name="tile_height" type="integer" label="Tile height" value="96" min="1" />
70 <param name="tile_width" type="integer" label="Tile width" value="96" min="1" />
71 <param name="chunk_depth" type="integer" label="Chunk depth" value="1" min="1" />
72 <param name="downsample_type" type="select" label="Downsampling method" multiple="false" >
73 <option value="SIMPLE" selected="true">SIMPLE</option>
74 <option value="GAUSSIAN" selected="false">GAUSSIAN</option>
75 <option value="AREA" selected="false">AREA</option>
76 <option value="LINEAR" selected="false">LINEAR</option>
77 <option value="CUBIC" selected="false">CUBIC</option>
78 <option value="LANCZOS" selected="false">LANCZOS</option>
79 </param>
80 <param name="compression" type="select" label="Compression method" multiple="false" >
81 <option value="null" selected="false">null</option>
82 <option value="zlib" selected="false">zlib</option>
83 <option value="blosc" selected="true">blosc</option>
84 </param>
85 <param name="dimension_order" type="select" label="Dimension order" multiple="false">
86 <option value="keep input order" selected="true">keep input order</option>
87 <option value="XYZCT" selected="false">XYZCT</option>
88 <option value="XYZTC" selected="false">XYZTC</option>
89 <option value="XYCTZ" selected="false">XYCTZ</option>
90 <option value="XYCZT" selected="false">XYCZT</option>
91 <option value="XYTCZ" selected="false">XYTCZ</option>
92 <option value="XYTZC" selected="false">XYTZC</option>
93 </param>
94 <param name="nesting" type="boolean" label="Use ' / ' as chunk path separator" truevalue="" falsevalue="--no-nested" checked="true" />
95 <param name="omefolder" type="boolean" label="Export OME metadata" truevalue="" falsevalue="--no-ome-meta-export" checked="true" />
96 <param name="droptop" type="boolean" label="Drop the series layer in the OME-Zarr folder hierarchy" truevalue="--scale-format-string '%2$d'" falsevalue="" checked="false" />
97 </section>
98 </inputs>
99 <outputs>
100 <data name="output" format="html" label="OME-Zarr Output" />
101 </outputs>
102 <tests>
103 <test expect_num_outputs="1">
104 <section name="io_options">
105 <param name="input" value="xyz_8bit__mitotic_plate_calibrated.tif"/>
106 <param name="output_name" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr" />
107 </section>
108 <output name="output" ftype="html">
109 <extra_files type="file" name="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" />
110 </output>
111 </test>
112 <test expect_num_outputs="1">
113 <section name="io_options">
114 <param name="input" value="coins.png"/>
115 <param name="output_name" value="coins.ome.zarr" />
116 </section>
117 <output name="output" ftype="html">
118 <extra_files type="file" name="coins.ome.zarr/.zgroup" value="coins.ome.zarr/.zgroup" />
119 </output>
120 </test>
121 <test expect_num_outputs="1">
122 <section name="io_options">
123 <param name="input" value="camera.jpg"/>
124 <param name="output_name" value="camera.ome.zarr" />
125 </section>
126 <output name="output" ftype="html">
127 <extra_files type="file" name="camera.ome.zarr/.zattrs" value="camera.ome.zarr/.zattrs" />
128 </output>
129 </test>
130 </tests>
131 <help>
132
133 **Converts images to OME-Zarr.**
134
135 Bioformats-based tool that converts a wide range of image file formats to the cloud-optimised format
136 OME-Zarr following the `OME-NGFF`_ specification.
137
138 .. _OME-NGFF: https://ngff.openmicroscopy.org/latest
139
140 </help>
141 <citations>
142 <citation type="doi">https://doi.org/10.5281/zenodo.5548102 </citation>
143 </citations>
144 </tool>