Mercurial > repos > imgteam > bfconvert

changeset 7:fa8ce46a95bb draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit 4eea5324bf5d02e6ac21006db677dd5a8ecbaaa2
author imgteam
date Thu, 12 Feb 2026 11:55:09 +0000
parents fcadded98e61
children
files bfconvert.xml creators.xml
diffstat 2 files changed, 26 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/bfconvert.xml	Thu Apr 04 15:23:54 2024 +0000
+++ b/bfconvert.xml	Thu Feb 12 11:55:09 2026 +0000
@@ -4,7 +4,7 @@
         <import>creators.xml</import>
         <import>tests.xml</import>
         <token name="@TOOL_VERSION@">6.7.0</token>
-        <token name="@VERSION_SUFFIX@">3</token>
+        <token name="@VERSION_SUFFIX@">4</token>
     </macros>
     <creator>
         <expand macro="creators/alliecreason"/>
@@ -21,6 +21,8 @@
     </requirements>
     <command> 
         <![CDATA[  
+        ln -s '$input_file' 'input.$input_file.ext' &&
+        
         bfconvert  
         #if $series_options['extract'] == 'True'
           -series $series_options.series
@@ -52,12 +54,12 @@
         #if $compression != 'False'
           -compression $compression
         #end if  
-        '$input_file' './res.$out_format' &&
+        'input.$input_file.ext' './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 label="Input Image" name="input_file" type="data" format="scn,ndpi,tf8,vms,xml,pcx,xml,binary,hdr,mov,psd,ome.tiff,tiff,pbm,nrrd,pgm,ppm,txt,tf2,zip,top,gif,wav,bmp,png,gz,cif,fli,btf,jpg,avi,html,sif,ome.tiff,par,fits,jp2,eps,nhdr,svs,mrc"/>
         <param name="out_format" type="select" label="Output data type">
             <option value="tiff" selected="True">TIFF</option>
             <option value="png">PNG</option>
--- a/creators.xml	Thu Apr 04 15:23:54 2024 +0000
+++ b/creators.xml	Thu Feb 12 11:55:09 2026 +0000
@@ -5,6 +5,16 @@
         <yield />
     </xml>
 
+    <xml name="creators/kostrykin">
+        <person givenName="Leonid" familyName="Kostrykin"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/rmassei">
+        <person givenName="Riccardo" familyName="Massei"/>
+        <yield/>
+    </xml>
+
     <xml name="creators/alliecreason">
         <person givenName="Allison" familyName="Creason"/>
         <yield/>
@@ -19,5 +29,15 @@
         <person givenName="Till" familyName="Korten"/>
         <yield/>
     </xml>
-    
+
+    <xml name="creators/pavanvidem">
+        <person givenName="Pavan" familyName="Videm"/>
+        <yield/>
+    </xml>
+
+    <xml name="creators/tuncK">
+        <person givenName="Tunc" familyName="Kayikcioglu"/>
+        <yield/>
+    </xml>
+
 </macros>