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comparison bf2raw.xml @ 0:4b6c2135e547 draft

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planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
author imgteam
date Wed, 15 Nov 2023 15:14:17 +0000
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children b32f5368e279
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-1:000000000000 0:4b6c2135e547
1 <tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>with Bioformats</description>
3 <macros>
4 <token name="@TOOL_VERSION@">0.7.0</token>
5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros>
7 <edam_operations>
8 <edam_operation>operation_3443</edam_operation>
9 </edam_operations>
10 <requirements>
11 <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container>
12 </requirements>
13 <command><![CDATA[
14
15 if [ ! -d $output.extra_files_path ];then
16 mkdir -p $output.extra_files_path;
17 fi;
18
19 #if str($io_options.input.ext)=='html':
20 #set dirlist=os.listdir($io_options.input.extra_files_path)
21 #assert len($dirlist) > 0
22 #set input_path=os.path.join(str($io_options.input.extra_files_path), str($dirlist[0]))
23 #else:
24 #set input_path=$io_options.input
25 #end if
26
27 bioformats2raw $input_path $output.extra_files_path/$io_options.output_name
28 #if $bf2raw_params.multiscales['options'] == 'auto':
29 --target-min-size $bf2raw_params.multiscales.min_xy_size
30 #elif $bf2raw_params.multiscales['options'] == 'manual':
31 --resolutions $bf2raw_params.resolutions
32 #end if
33 --tile_height $bf2raw_params.tile_height
34 --tile_width $bf2raw_params.tile_width
35 --chunk_depth $bf2raw_params.chunk_depth
36 --downsample-type $bf2raw_params.downsample_type
37 --compression $bf2raw_params.compression
38 --max_workers "\${GALAXY_SLOTS:-4}"
39 $bf2raw_params.nesting
40 $bf2raw_params.omefolder
41 $bf2raw_params.droptop
42 #if not str($bf2raw_params.dimension_order) == 'keep input order':
43 --dimension-order $bf2raw_params.dimension_order
44 #end if
45 ###--overwrite
46 --debug off &> /dev/null;
47
48 ]]></command>
49 <inputs>
50 <section name="io_options" title="Input-output paths">
51 <param name="input" type="data" format="atsf,scn,ali,labels,ffr,jpeg,ndpi,tf8,pty,fff,mnc,vms,mng,xml,pcx,img,pct,ims,bip,ome.xml,bin,flex,his,hdr,mov,psd,spi,ipl,dv,aiix,j2kr,pst,mod,ome.tif,tif,obf,dib,dic,im3,tga,pbm,c01,crw,mrcs,l2d,seq,mdb,cfg,htm,mvd2,arf,vsi,companion.ome,htd,aim,fts,ndpis,r3d.log,nef,res,jpx,ics,rec,nd2,cr2,dcm,mea,ome,lei,lms,j2k,oib,mtb,ima,ets,wlz,pict,sm3,sm2,nrrd,xdce,acff,al3d,zvi,1sc,xys,tiff,pgm,pcoraw,ppm,ipm,set,cxd,ipw,apl,fake,tnb,txt,xv,tf2,ps,log,zip,epsi,j2ki,dicom,top,msr,frm,hed,gif,dm2,dm3,dm4,zpo,wav,wat,2fl,sdt,liff,hx,pic,ome.btf,am,bmp,pnl,r3d_d3d,jpf,png,tfr,dti,nii.gz,cif,fdf,grey,df3,stk,fli,hdf,btf,stp,ch5,v,sld,ids,dv.log,jpk,mrw,r3d,xlog,ano,jpe,sxm,jpg,vws,raw,czi,spl,avi,ome.tf8,inf,spc,ome.tf2,spe,lsm,afm,lif,naf,afi,inr,lim,nd,tim,html,sif,env,tif,csv,map,nii,gel,ome.tiff,oif,par,amiramesh,pr3,fits,lut,jp2,oir,dat,aisf,zfr,zfp,xqd,eps,xqf,st,nhdr,i2i,thm,exp,svs,mrc" label="Input image located in Galaxy history"/>
52 <param name="output_name" type="text" value="data.zarr" label="Output zarr data"/>
53 </section>
54 <section name="bf2raw_params" title="Parameters fed to file conversion module">
55 <conditional name="multiscales" >
56 <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" >
57 <option value="auto" selected="true">auto</option>
58 <option value="manual" selected="false">manual</option>
59 </param>
60 <when value="auto">
61 <param name="min_xy_size" type="integer" min="1" optional="true" label="Min x-y dimension for the lowest resolution" value="256" />
62 </when>
63 <when value="manual">
64 <param name="resolution_count" type="integer" min="1" optional="true" label="Number of resolution layers" value="3"/>
65 </when>
66 </conditional >
67 <param name="tile_height" type="integer" label="Tile height" value="96" min="1" />
68 <param name="tile_width" type="integer" label="Tile width" value="96" min="1" />
69 <param name="chunk_depth" type="integer" label="Chunk depth" value="1" min="1" />
70 <param name="downsample_type" type="select" label="Downsampling method" multiple="false" >
71 <option value="SIMPLE" selected="true">SIMPLE</option>
72 <option value="GAUSSIAN" selected="false">GAUSSIAN</option>
73 <option value="AREA" selected="false">AREA</option>
74 <option value="LINEAR" selected="false">LINEAR</option>
75 <option value="CUBIC" selected="false">CUBIC</option>
76 <option value="LANCZOS" selected="false">LANCZOS</option>
77 </param>
78 <param name="compression" type="select" label="Compression method" multiple="false" >
79 <option value="null" selected="false">null</option>
80 <option value="zlib" selected="false">zlib</option>
81 <option value="blosc" selected="true">blosc</option>
82 </param>
83 <param name="dimension_order" type="select" label="Dimension order" multiple="false">
84 <option value="keep input order" selected="true">keep input order</option>
85 <option value="XYZCT" selected="false">XYZCT</option>
86 <option value="XYZTC" selected="false">XYZTC</option>
87 <option value="XYCTZ" selected="false">XYCTZ</option>
88 <option value="XYCZT" selected="false">XYCZT</option>
89 <option value="XYTCZ" selected="false">XYTCZ</option>
90 <option value="XYTZC" selected="false">XYTZC</option>
91 </param>
92 <param name="nesting" type="boolean" label="Use ' / ' as chunk path separator" truevalue="" falsevalue="--no-nested" checked="true" />
93 <param name="omefolder" type="boolean" label="Export OME metadata" truevalue="" falsevalue="--no-ome-meta-export" checked="true" />
94 <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" />
95 </section>
96 </inputs>
97 <outputs>
98 <data name="output" format="html" label="OME-Zarr Output" />
99 </outputs>
100 <tests>
101 <test expect_num_outputs="1">
102 <param name="input" value="xyz_8bit__mitotic_plate_calibrated.tif"/>
103 <param name="output_name" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr" />
104 <output name="output" ftype="html">
105 <extra_files type="file" name="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" />
106 </output>
107 </test>
108 <test expect_num_outputs="1">
109 <param name="input" value="astronaut.png"/>
110 <param name="output_name" value="astronaut.ome.zarr" />
111 <output name="output" ftype="html">
112 <extra_files type="file" name="astronaut.ome.zarr/.zgroup" value="astronaut.ome.zarr/.zgroup" />
113 </output>
114 </test>
115 <test expect_num_outputs="1">
116 <param name="input" value="rocket.jpg"/>
117 <param name="output_name" value="rocket.ome.zarr" />
118 <output name="output" ftype="html">
119 <extra_files type="file" name="rocket.ome.zarr/.zattrs" value="rocket.ome.zarr/.zattrs" />
120 </output>
121 </test>
122 </tests>
123 <help>
124 **What it does**
125
126 Bioformats-based tool that converts a wide range of image file formats to the cloud-optimised format OME-Zarr following the `OME-NGFF`_ specification.
127
128 .. _OME-NGFF: https://ngff.openmicroscopy.org/latest
129 </help>
130 <citations>
131 <citation type="doi">https://doi.org/10.5281/zenodo.5548102 </citation>
132 </citations>
133 </tool>