# HG changeset patch
# User imgteam
# Date 1663262344 0
# Node ID f3360fbeda6455d887f73f13ff4664740bf38b1e
# Parent  b07f4839ca7716b9b40838b5e57ee3e885d4c474
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 1ac9c3e967f78c0001833a4c4d7e877f234d4785

diff -r b07f4839ca77 -r f3360fbeda64 bfconvert.xml
--- a/bfconvert.xml	Mon Jul 22 13:34:12 2019 -0400
+++ b/bfconvert.xml	Thu Sep 15 17:19:04 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**
diff -r b07f4839ca77 -r f3360fbeda64 test-data/res.ome.tiff
Binary file test-data/res.ome.tiff has changed