Mercurial > repos > imgteam > bfconvert
changeset 3:802a235f1ad0 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 1ac9c3e967f78c0001833a4c4d7e877f234d4785
| author | imgteam |
|---|---|
| date | Thu, 15 Sep 2022 17:18:34 +0000 |
| parents | ba0a5567b446 |
| children | 86e519799f6c |
| files | bfconvert.xml test-data/res.ome.tiff |
| diffstat | 2 files changed, 117 insertions(+), 80 deletions(-) [+] |
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--- a/bfconvert.xml Mon Jul 22 13:33:52 2019 -0400 +++ b/bfconvert.xml Thu Sep 15 17:18:34 2022 +0000 @@ -1,123 +1,152 @@ -<tool id="ip_convertimage" name="Convert image" version="0.4"> +<tool id="ip_convertimage" name="Convert image" version="6.7.0+galaxy0"> <description>Convert image</description> <requirements> - <requirement type="package" version="5.7.1">bftools</requirement> + <requirement type="package" version="6.7.0">bftools</requirement> </requirements> <command> <![CDATA[ bfconvert #if $series_options['extract'] == 'True' - -series $series + -series $series_options.series #end if #if $timepoint_options['extract'] == 'True' - -timepoint $timepoint + -timepoint $timepoint_options.timepoint #end if #if $channel_options['extract'] == 'True' - -channel $channel + -channel $channel_options.channel #end if #if $z_options['extract'] == 'True' - -z $z + -z $z_options.z #end if #if $range_options['extract'] == 'True' - -range $range_lower $range_upper + -range $range_options.range_lower $range_options.range_upper #end if #if $crop_options['extract'] == 'True' - -crop $crop_x $crop_y $crop_width $crop_height + -crop "$crop_options.crop_x,$crop_options.crop_y,$crop_options.crop_width,$crop_options.crop_height" #end if #if $tile_options['extract'] == 'True' - -tilex $tile_x -tiley $tile_y + -tilex $tile_options.tile_x -tiley $tile_options.tile_y + #end if + #if $pyramid_options.generate == 'True' + -pyramid-resolutions $pyramid_options.pyramid_resolutions + -pyramid-scale $pyramid_options.pyramid_scale #end if - '$input_file' ./res.$out_format && - mv ./res.$out_format ./result_image + $bigtiff + $noflat + #if $compression != 'False' + -compression $compression + #end if + '$input_file' './res.$out_format' && + mv './res.$out_format' ./result_image ]]> </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> + <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"> - <option selected="True" value="False">All series</option> - <option value="True">Extract series</option> - </param> - <when value="False"> </when> - <when value="True"> - <param name="series" type="integer" value="0" label="Series id" /> - </when> + <param label="Extract series" name="extract" type="select"> + <option selected="True" value="False">All series</option> + <option value="True">Extract series</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="series" type="integer" value="0" label="Series id" /> + </when> </conditional> <conditional name="timepoint_options"> - <param label="Extract timepoint" name="extract" type="select"> - <option selected="True" value="False">All timepoints</option> - <option value="True">Extract timepoint</option> - </param> - <when value="False"> </when> - <when value="True"> - <param name="timepoint" type="integer" value="0" label="Timepoint id" /> - </when> + <param name="extract" type="select" label="Extract timepoint"> + <option selected="True" value="False">All timepoints</option> + <option value="True">Extract timepoint</option> + </param> + <when value="False"></when> + <when value="True"> + <param name="timepoint" type="integer" value="0" label="Timepoint ID" /> + </when> </conditional> <conditional name="channel_options"> - <param label="Extract channel" name="extract" type="select"> - <option selected="True" value="False">All channels</option> - <option value="True">Extract channel</option> - </param> - <when value="False"> </when> - <when value="True"> - <param name="channel" type="integer" value="0" label="Channel id" /> - </when> + <param name="extract" type="select" label="Extract channel" > + <option selected="True" value="False">All channels</option> + <option value="True">Extract channel</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="channel" type="integer" value="0" label="Channel id" /> + </when> </conditional> <conditional name="z_options"> - <param label="Extract z-slice" name="extract" type="select"> - <option selected="True" value="False">All z-slices</option> - <option value="True">Extract z-slice</option> - </param> - <when value="False"> </when> - <when value="True"> - <param name="z" type="integer" value="0" label="Z-slice id" /> - </when> + <param label="Extract z-slice" name="extract" type="select"> + <option selected="True" value="False">All z-slices</option> + <option value="True">Extract z-slice</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="z" type="integer" value="0" label="Z-slice id" /> + </when> </conditional> <conditional name="range_options"> - <param label="Extract range" name="extract" type="select"> - <option selected="True" value="False">All images</option> - <option value="True">Extract range by indicess (inclusive)</option> - </param> - <when value="False"> </when> - <when value="True"> - <param name="range_lower" type="integer" value="0" label="Lower image id" /> - <param name="range_upper" type="integer" value="1" label="Upper image id" /> - </when> + <param label="Extract range" name="extract" type="select"> + <option selected="True" value="False">All images</option> + <option value="True">Extract range by indicess (inclusive)</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="range_lower" type="integer" value="0" label="Lower image id" /> + <param name="range_upper" type="integer" value="1" label="Upper image id" /> + </when> </conditional> <conditional name="crop_options"> - <param label="Extract crop" name="extract" type="select"> - <option selected="True" value="False">Full image</option> - <option value="True">Extract crop</option> - </param> - <when value="False"> </when> - <when value="True"> - <param name="crop_x" type="integer" value="0" label="X" /> - <param name="crop_y" type="integer" value="0" label="Y" /> - <param name="crop_width" type="integer" value="512" label="Width" /> - <param name="crop_height" type="integer" value="512" label="height" /> - </when> + <param label="Extract crop" name="extract" type="select"> + <option selected="True" value="False">Full image</option> + <option value="True">Extract crop</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="crop_x" type="integer" value="0" label="X" /> + <param name="crop_y" type="integer" value="0" label="Y" /> + <param name="crop_width" type="integer" value="512" label="Width" /> + <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> + <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> + <conditional name="pyramid_options"> + <param label="Pyramid image" name="generate" type="select"> + <option selected="True" value="True">Generate Pyramid</option> + <option value="False">No Pyramid</option> + </param> + <when value="True"> + <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/> + <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" /> + </when> + </conditional> + <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/> + <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/> + <param label="Compression" name="compression" type="select"> + <option selected="True" value="False">No Compression</option> + <option value="LZW">LZW</option> + <option value="JPEG-2000">JPEG-2000</option> + <option value="JPEG-2000 Lossy">JPEG-2000 Lossy</option> + <option value="JPEG">JPEG</option> + <option value="zlib">zlib</option> + </param> </inputs> <outputs> <data format="tiff" name="output" from_work_dir="result_image"> @@ -125,7 +154,7 @@ <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="ome.tiff" format="ome.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" /> @@ -138,6 +167,14 @@ <param name="out_format" value="tiff" /> <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/> </test> + <test> + <param name="input_file" value="input.png" /> + <param name="out_format" value="ome.tiff" /> + <param name="pyramid_options.generate" value="True"/> + <param name="pyramid_options.pyramid_resolutions" value="4"/> + <param name="pyramid_options.pyramid_scale" value="2"/> + <output name="output" value="res.ome.tiff" ftype="ome.tiff" compare="sim_size"/> + </test> </tests> <help> **What it does**