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annotate 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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0
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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1 <tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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2 <description>with Bioformats</description>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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3 <macros>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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4 <token name="@TOOL_VERSION@">0.7.0</token>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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5 <token name="@VERSION_SUFFIX@">0</token>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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6 </macros>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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7 <edam_operations>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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8 <edam_operation>operation_3443</edam_operation>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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9 </edam_operations>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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10 <requirements>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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11 <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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12 </requirements>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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13 <command><![CDATA[
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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14
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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15 if [ ! -d $output.extra_files_path ];then
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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16 mkdir -p $output.extra_files_path;
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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17 fi;
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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18
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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19 #if str($io_options.input.ext)=='html':
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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20 #set dirlist=os.listdir($io_options.input.extra_files_path)
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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21 #assert len($dirlist) > 0
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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22 #set input_path=os.path.join(str($io_options.input.extra_files_path), str($dirlist[0]))
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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23 #else:
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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24 #set input_path=$io_options.input
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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25 #end if
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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26
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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27 bioformats2raw $input_path $output.extra_files_path/$io_options.output_name
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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28 #if $bf2raw_params.multiscales['options'] == 'auto':
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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29 --target-min-size $bf2raw_params.multiscales.min_xy_size
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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30 #elif $bf2raw_params.multiscales['options'] == 'manual':
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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31 --resolutions $bf2raw_params.resolutions
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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32 #end if
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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33 --tile_height $bf2raw_params.tile_height
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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34 --tile_width $bf2raw_params.tile_width
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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35 --chunk_depth $bf2raw_params.chunk_depth
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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36 --downsample-type $bf2raw_params.downsample_type
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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37 --compression $bf2raw_params.compression
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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38 --max_workers "\${GALAXY_SLOTS:-4}"
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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39 $bf2raw_params.nesting
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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40 $bf2raw_params.omefolder
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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41 $bf2raw_params.droptop
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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42 #if not str($bf2raw_params.dimension_order) == 'keep input order':
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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43 --dimension-order $bf2raw_params.dimension_order
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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44 #end if
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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45 ###--overwrite
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46 --debug off &> /dev/null;
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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47
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48 ]]></command>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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49 <inputs>
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50 <section name="io_options" title="Input-output paths">
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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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"/>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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52 <param name="output_name" type="text" value="data.zarr" label="Output zarr data"/>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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53 </section>
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54 <section name="bf2raw_params" title="Parameters fed to file conversion module">
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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55 <conditional name="multiscales" >
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56 <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" >
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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57 <option value="auto" selected="true">auto</option>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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58 <option value="manual" selected="false">manual</option>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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59 </param>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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60 <when value="auto">
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61 <param name="min_xy_size" type="integer" min="1" optional="true" label="Min x-y dimension for the lowest resolution" value="256" />
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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62 </when>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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63 <when value="manual">
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64 <param name="resolution_count" type="integer" min="1" optional="true" label="Number of resolution layers" value="3"/>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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65 </when>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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66 </conditional >
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67 <param name="tile_height" type="integer" label="Tile height" value="96" min="1" />
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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68 <param name="tile_width" type="integer" label="Tile width" value="96" min="1" />
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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69 <param name="chunk_depth" type="integer" label="Chunk depth" value="1" min="1" />
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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70 <param name="downsample_type" type="select" label="Downsampling method" multiple="false" >
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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71 <option value="SIMPLE" selected="true">SIMPLE</option>
4b6c2135e547 planemo upload for repository https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/tree/main/tools/bioformats2raw commit f7ffeafe5d1fd78de014c7dfda75f000f9e2e5d1
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72 <option value="GAUSSIAN" selected="false">GAUSSIAN</option>
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73 <option value="AREA" selected="false">AREA</option>
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74 <option value="LINEAR" selected="false">LINEAR</option>
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75 <option value="CUBIC" selected="false">CUBIC</option>
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76 <option value="LANCZOS" selected="false">LANCZOS</option>
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77 </param>
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78 <param name="compression" type="select" label="Compression method" multiple="false" >
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79 <option value="null" selected="false">null</option>
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80 <option value="zlib" selected="false">zlib</option>
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81 <option value="blosc" selected="true">blosc</option>
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82 </param>
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83 <param name="dimension_order" type="select" label="Dimension order" multiple="false">
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84 <option value="keep input order" selected="true">keep input order</option>
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85 <option value="XYZCT" selected="false">XYZCT</option>
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86 <option value="XYZTC" selected="false">XYZTC</option>
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87 <option value="XYCTZ" selected="false">XYCTZ</option>
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88 <option value="XYCZT" selected="false">XYCZT</option>
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89 <option value="XYTCZ" selected="false">XYTCZ</option>
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90 <option value="XYTZC" selected="false">XYTZC</option>
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91 </param>
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92 <param name="nesting" type="boolean" label="Use ' / ' as chunk path separator" truevalue="" falsevalue="--no-nested" checked="true" />
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93 <param name="omefolder" type="boolean" label="Export OME metadata" truevalue="" falsevalue="--no-ome-meta-export" checked="true" />
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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" />
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95 </section>
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96 </inputs>
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97 <outputs>
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98 <data name="output" format="html" label="OME-Zarr Output" />
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99 </outputs>
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100 <tests>
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101 <test expect_num_outputs="1">
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102 <param name="input" value="xyz_8bit__mitotic_plate_calibrated.tif"/>
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103 <param name="output_name" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr" />
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104 <output name="output" ftype="html">
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105 <extra_files type="file" name="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" />
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106 </output>
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107 </test>
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108 <test expect_num_outputs="1">
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109 <param name="input" value="astronaut.png"/>
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110 <param name="output_name" value="astronaut.ome.zarr" />
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111 <output name="output" ftype="html">
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112 <extra_files type="file" name="astronaut.ome.zarr/.zgroup" value="astronaut.ome.zarr/.zgroup" />
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113 </output>
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114 </test>
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115 <test expect_num_outputs="1">
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116 <param name="input" value="rocket.jpg"/>
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117 <param name="output_name" value="rocket.ome.zarr" />
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118 <output name="output" ftype="html">
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119 <extra_files type="file" name="rocket.ome.zarr/.zattrs" value="rocket.ome.zarr/.zattrs" />
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120 </output>
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121 </test>
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122 </tests>
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123 <help>
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124 **What it does**
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125
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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.
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127
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128 .. _OME-NGFF: https://ngff.openmicroscopy.org/latest
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129 </help>
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130 <citations>
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131 <citation type="doi">https://doi.org/10.5281/zenodo.5548102 </citation>
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132 </citations>
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133 </tool>