comparison bfconvert.xml @ 4:10eed33aa9b2 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit e27798cf1f9eb7fd34bf9b6fce21f6825f3872a1

3:f3360fbeda64

<tool id="ip_convertimage" name="Convert image" version="6.7.0+galaxy0"> 
  <description>Convert image</description>
  <requirements>
      <requirement type="package" version="6.7.0">bftools</requirement>
  </requirements>
  <command> 

          -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_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
        $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="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>

            <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**

4:10eed33aa9b2

<tool id="ip_convertimage" name="Convert image" version="6.7.0+galaxy1"> 
  <description>Convert image</description>
  <requirements>
      <requirement type="package" version="6.7.0">bftools</requirement>
  </requirements>
  <command> 

          -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_options.tile_x -tiley $tile_options.tile_y
        #end if
        #if $pyramid_options.generate == 'True' and $out_format not in ['png', 'jpg', 'eps', 'avi']
          -pyramid-resolutions $pyramid_options.pyramid_resolutions
          -pyramid-scale $pyramid_options.pyramid_scale
        #end if
        $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="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>

            <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" />
            <conditional name="pyramid_options">
                <param name="generate" value="True"/>
                <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"/>
        </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"/>
        </test>
  </tests>    
  <help>
    **What it does**