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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit 4eea5324bf5d02e6ac21006db677dd5a8ecbaaa2
author imgteam
date Thu, 12 Feb 2026 11:55:09 +0000
parents fcadded98e61
children
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6:fcadded98e61 7:fa8ce46a95bb
2 <description>with Bioformats</description> 2 <description>with Bioformats</description>
3 <macros> 3 <macros>
4 <import>creators.xml</import> 4 <import>creators.xml</import>
5 <import>tests.xml</import> 5 <import>tests.xml</import>
6 <token name="@TOOL_VERSION@">6.7.0</token> 6 <token name="@TOOL_VERSION@">6.7.0</token>
7 <token name="@VERSION_SUFFIX@">3</token> 7 <token name="@VERSION_SUFFIX@">4</token>
8 </macros> 8 </macros>
9 <creator> 9 <creator>
10 <expand macro="creators/alliecreason"/> 10 <expand macro="creators/alliecreason"/>
11 <expand macro="creators/bmcv"/> 11 <expand macro="creators/bmcv"/>
12 </creator> 12 </creator>
19 <requirements> 19 <requirements>
20 <requirement type="package" version="@TOOL_VERSION@">bftools</requirement> 20 <requirement type="package" version="@TOOL_VERSION@">bftools</requirement>
21 </requirements> 21 </requirements>
22 <command> 22 <command>
23 <![CDATA[ 23 <![CDATA[
24 ln -s '$input_file' 'input.$input_file.ext' &&
25
24 bfconvert 26 bfconvert
25 #if $series_options['extract'] == 'True' 27 #if $series_options['extract'] == 'True'
26 -series $series_options.series 28 -series $series_options.series
27 #end if 29 #end if
28 #if $timepoint_options['extract'] == 'True' 30 #if $timepoint_options['extract'] == 'True'
50 $bigtiff 52 $bigtiff
51 $noflat 53 $noflat
52 #if $compression != 'False' 54 #if $compression != 'False'
53 -compression $compression 55 -compression $compression
54 #end if 56 #end if
55 '$input_file' './res.$out_format' && 57 'input.$input_file.ext' './res.$out_format' &&
56 mv './res.$out_format' ./result_image 58 mv './res.$out_format' ./result_image
57 ]]> 59 ]]>
58 </command> 60 </command>
59 <inputs> 61 <inputs>
60 <param label="Input Image" name="input_file" 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"/> 62 <param label="Input Image" name="input_file" type="data" format="scn,ndpi,tf8,vms,xml,pcx,xml,binary,hdr,mov,psd,ome.tiff,tiff,pbm,nrrd,pgm,ppm,txt,tf2,zip,top,gif,wav,bmp,png,gz,cif,fli,btf,jpg,avi,html,sif,ome.tiff,par,fits,jp2,eps,nhdr,svs,mrc"/>
61 <param name="out_format" type="select" label="Output data type"> 63 <param name="out_format" type="select" label="Output data type">
62 <option value="tiff" selected="True">TIFF</option> 64 <option value="tiff" selected="True">TIFF</option>
63 <option value="png">PNG</option> 65 <option value="png">PNG</option>
64 <option value="jpg">JPEG</option> 66 <option value="jpg">JPEG</option>
65 <option value="ome.tiff">OME TIFF</option> 67 <option value="ome.tiff">OME TIFF</option>