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comparison bf2raw.xml @ 2:1b3e7d53cec6 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit ae73350d8f8f232cf598bbcf411778dc1de594f6
author imgteam
date Mon, 26 Feb 2024 20:01:43 +0000
parents b32f5368e279
children 94fe1169328c
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1:b32f5368e279 2:1b3e7d53cec6
1 <tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>with Bioformats</description> 2 <description>with Bioformats</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.7.0</token> 4 <token name="@TOOL_VERSION@">0.7.0</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 </macros> 6 </macros>
7 <edam_operations> 7 <edam_operations>
8 <edam_operation>operation_3443</edam_operation> 8 <edam_operation>operation_3443</edam_operation>
9 </edam_operations> 9 </edam_operations>
10 <requirements> 10 <requirements>
11 <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container> 11 <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container>
12 </requirements> 12 </requirements>
13 <command><![CDATA[ 13 <command><![CDATA[
14
15 if [ ! -d $output.files_path ];then 14 if [ ! -d $output.files_path ];then
16 mkdir -p $output.files_path; 15 mkdir -p $output.files_path;
17 fi; 16 fi;
18 17
19 #if str($io_options.input.ext)=='html': 18 #if str($io_options.input.ext)=='html':
22 #set input_path=os.path.join(str($io_options.input.files_path), str($dirlist[0])) 21 #set input_path=os.path.join(str($io_options.input.files_path), str($dirlist[0]))
23 #else: 22 #else:
24 #set input_path=$io_options.input 23 #set input_path=$io_options.input
25 #end if 24 #end if
26 25
27 bioformats2raw $input_path $output.files_path/$io_options.output_name 26 export _JAVA_OPTIONS="-Djava.io.tmpdir=/usr/local/man/" && bioformats2raw $input_path $output.files_path/$io_options.output_name
28 #if $bf2raw_params.multiscales['options'] == 'auto': 27 #if $bf2raw_params.multiscales['options'] == 'auto':
29 --target-min-size $bf2raw_params.multiscales.min_xy_size 28 --target-min-size $bf2raw_params.multiscales.min_xy_size
30 #elif $bf2raw_params.multiscales['options'] == 'manual': 29 #elif $bf2raw_params.multiscales['options'] == 'manual':
31 --resolutions $bf2raw_params.resolutions 30 --resolutions $bf2raw_params.resolutions
32 #end if 31 #end if
40 $bf2raw_params.omefolder 39 $bf2raw_params.omefolder
41 $bf2raw_params.droptop 40 $bf2raw_params.droptop
42 #if not str($bf2raw_params.dimension_order) == 'keep input order': 41 #if not str($bf2raw_params.dimension_order) == 'keep input order':
43 --dimension-order $bf2raw_params.dimension_order 42 --dimension-order $bf2raw_params.dimension_order
44 #end if 43 #end if
45 ###--overwrite 44 --overwrite &> /dev/null;
46 --debug off &> /dev/null;
47 45
48 ]]></command> 46 ]]></command>
49 <inputs> 47 <inputs>
50 <section name="io_options" title="Input-output paths" expanded="true"> 48 <section name="io_options" title="Input-output paths" expanded="true">
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"/> 49 <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="output.ome.zarr" label="Output zarr data"/> 50 <param name="output_name" type="text" value="output.ome.zarr" label="Name of the generated OME-Zarr"/>
53 </section> 51 </section>
54 <section name="bf2raw_params" title="Parameters fed to file conversion module"> 52 <section name="bf2raw_params" title="Parameters fed to file conversion module">
55 <conditional name="multiscales" > 53 <conditional name="multiscales" >
56 <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" > 54 <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" >
57 <option value="auto" selected="true">auto</option> 55 <option value="auto" selected="true">auto</option>