Mercurial > repos > imgteam > bfconvert
diff bfconvert.xml @ 6:fcadded98e61 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
| author | imgteam |
|---|---|
| date | Thu, 04 Apr 2024 15:23:54 +0000 |
| parents | 85edbb7a436b |
| children |
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--- a/bfconvert.xml Fri Nov 10 14:23:17 2023 +0000 +++ b/bfconvert.xml Thu Apr 04 15:23:54 2024 +0000 @@ -1,15 +1,25 @@ -<tool id="ip_convertimage" name="Convert image format" version="6.7.0+galaxy2"> - <description>with Bioformats</description> - <edam_operations> - <edam_operation>operation_3443</edam_operation> - </edam_operations> - <xrefs> - <xref type="biii">python-bioformats</xref> - </xrefs> - <requirements> - <requirement type="package" version="6.7.0">bftools</requirement> - </requirements> - <command> +<tool id="ip_convertimage" name="Convert image format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> + <description>with Bioformats</description> + <macros> + <import>creators.xml</import> + <import>tests.xml</import> + <token name="@TOOL_VERSION@">6.7.0</token> + <token name="@VERSION_SUFFIX@">3</token> + </macros> + <creator> + <expand macro="creators/alliecreason"/> + <expand macro="creators/bmcv"/> + </creator> + <edam_operations> + <edam_operation>operation_3443</edam_operation> + </edam_operations> + <xrefs> + <xref type="biii">python-bioformats</xref> + </xrefs> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">bftools</requirement> + </requirements> + <command> <![CDATA[ bfconvert #if $series_options['extract'] == 'True' @@ -45,134 +55,134 @@ '$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> - </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> - </conditional> - <conditional name="timepoint_options"> - <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 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> - </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> + </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> - <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> - </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> - <conditional name="pyramid_options"> - <param label="Pyramid image" name="generate" type="select" help="Pyramids will be generated only if the selected output format supports pyramids (OME TIFF, JPEG 2000)."><!-- see: https://docs.openmicroscopy.org/bio-formats/6.7.0/supported-formats.html --> - <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> - <when value="False" /> - </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"> - <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="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" /> - </change_format> - </data> - </outputs> - <tests> + + <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> + </conditional> + <conditional name="timepoint_options"> + <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 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> + </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> + </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> + </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> + <conditional name="pyramid_options"> + <param label="Pyramid image" name="generate" type="select" help="Pyramids will be generated only if the selected output format supports pyramids (OME TIFF, JPEG 2000)."><!-- see: https://docs.openmicroscopy.org/bio-formats/6.7.0/supported-formats.html --> + <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> + <when value="False" /> + </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"> + <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="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" /> + </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"/> + <param name="out_format" value="tiff" /> + <expand macro="tests/intensity_image_diff" name="output" value="res.tiff" ftype="tiff"/> </test> <test> <param name="input_file" value="input.png" /> @@ -182,18 +192,20 @@ <param name="pyramid_resolutions" value="4"/> <param name="pyramid_scale" value="2"/> </conditional> - <output name="output" value="res.ome.tiff" ftype="ome.tiff" compare="sim_size"/> + <expand macro="tests/intensity_image_diff" name="output" value="res.ome.tiff" ftype="ome.tiff"/> </test> <test> <param name="input_file" value="input.tiff" /> <param name="out_format" value="png" /> - <output name="output" value="input.tiff.png" ftype="png" compare="sim_size"/> + <expand macro="tests/intensity_image_diff" name="output" value="input.tiff.png" ftype="png"/> </test> - </tests> - <help> - **What it does** + </tests> + <help> - Universial image converter using bioformats. + **Converts image format.** + + Universial image converter using bioformats. + </help> <citations> <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>