Mercurial > repos > imgteam > bfconvert
changeset 1:6317c4a379b2 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
| author | imgteam |
|---|---|
| date | Mon, 22 Jul 2019 12:45:14 -0400 |
| parents | bbb307f731c3 |
| children | b07f4839ca77 |
| files | bfconvert.xml |
| diffstat | 1 files changed, 37 insertions(+), 4 deletions(-) [+] |
line wrap: on
line diff
--- a/bfconvert.xml Mon Jul 22 11:09:08 2019 -0400 +++ b/bfconvert.xml Mon Jul 22 12:45:14 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="ip_convertimage" name="Convert image" version="0.1"> +<tool id="ip_convertimage" name="Convert image" version="0.3"> <description>Convert image</description> <requirements> <requirement type="package" version="5.7.1">bftools</requirement> @@ -24,11 +24,23 @@ #if $crop_options['extract'] == 'True' -crop $crop_x $crop_y $crop_width $crop_height #end if - '$input_file' ./res.tiff + #if $tile_options['extract'] == 'True' + -tilex $tile_x -tiley $tile_y + #end if + '$input_file' ./res.$out_format ]]> </command> <inputs> <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"/> + <param name="out_format" type="select" label="Output data type"> + <option value="tiff" selected="True">TIFF</option> + <option value="png">PNG</option> + <option value="jpg">JPEG</option> + <option value="ome.tiff">OME TIFF</option> + <option value="jp2">JPEG 2000</option> + <option value="eps">EPS</option> + <option value="avi">AVI</option> + </param> <conditional name="series_options"> <param label="Extract series" name="extract" type="select"> @@ -94,14 +106,35 @@ <param name="crop_height" type="integer" value="512" label="height" /> </when> </conditional> - + <conditional name="tile_options"> + <param label="Tile image" name="extract" type="select"> + <option selected="True" value="False">No tiling</option> + <option value="True">Tile image</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="tile_x" type="integer" value="512 " label="Tile width" /> + <param name="tile_y" type="integer" value="512 " label="Tile height" /> + </when> + </conditional> </inputs> <outputs> - <data format="tiff" name="output" from_work_dir="res.tiff"/> + <data format="tiff" name="output" from_work_dir="res.tiff"> + <change_format> + <when input="out_format" value="tiff" format="tiff" /> + <when input="out_format" value="png" format="png" /> + <when input="out_format" value="jpg" format="jpg" /> + <when input="out_format" value="ome.tiff" format="tiff" /> + <when input="out_format" value="jp2" format="jpg" /> + <when input="out_format" value="eps" format="eps" /> + <when input="out_format" value="avi" format="avi" /> + </change_format> + </data> </outputs> <tests> <test> <param name="input_file" value="input.png" /> + <param name="out_format" value="tiff" /> <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/> </test> </tests>