annotate bfconvert.xml @ 6:fcadded98e61 draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit c045f067a57e8308308cf6329060c7ccd3fc372f

<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'
          -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" />
            <expand macro="tests/intensity_image_diff" name="output" value="res.tiff" ftype="tiff"/>
        </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>
            <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" />
            <expand macro="tests/intensity_image_diff" name="output" value="input.tiff.png" ftype="png"/>
        </test>
    </tests>    
    <help>

        **Converts image format.**

        Universial image converter using bioformats.

    </help>
    <citations>
        <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
    </citations>
</tool>