annotate bfconvert.xml @ 4:10eed33aa9b2 draft

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

<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> 
        <![CDATA[  
        bfconvert  
        #if $series_options['extract'] == 'True'
          -series $series_options.series
        #end if
        #if $timepoint_options['extract'] == 'True'
          -timepoint $timepoint_options.timepoint
        #end if
        #if $channel_options['extract'] == 'True'
          -channel $channel_options.channel
        #end if
        #if $z_options['extract'] == 'True'
          -z $z_options.z
        #end if
        #if $range_options['extract'] == 'True'
          -range $range_options.range_lower $range_options.range_upper
        #end if
        #if $crop_options['extract'] == 'True'
          -crop "$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="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>
        </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"/>
        </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**

   Universial image converter using bioformats.
    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>