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Fix bioformats2raw tool #102

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merged 2 commits into from
Feb 26, 2024
Merged

Fix bioformats2raw tool #102

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5264ada
Fix bf2raw
kostrykin Feb 26, 2024
38fe99e
Update label of `output_name`
kostrykin Feb 26, 2024
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10 changes: 4 additions & 6 deletions tools/bioformats2raw/bf2raw.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
<description>with Bioformats</description>
<macros>
<token name="@TOOL_VERSION@">0.7.0</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
</macros>
<edam_operations>
<edam_operation>operation_3443</edam_operation>
Expand All @@ -11,7 +11,6 @@
<container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container>
</requirements>
<command><![CDATA[

if [ ! -d $output.files_path ];then
mkdir -p $output.files_path;
fi;
Expand All @@ -24,7 +23,7 @@ fi;
#set input_path=$io_options.input
#end if

bioformats2raw $input_path $output.files_path/$io_options.output_name
export _JAVA_OPTIONS="-Djava.io.tmpdir=/usr/local/man/" && bioformats2raw $input_path $output.files_path/$io_options.output_name
#if $bf2raw_params.multiscales['options'] == 'auto':
--target-min-size $bf2raw_params.multiscales.min_xy_size
#elif $bf2raw_params.multiscales['options'] == 'manual':
Expand All @@ -42,14 +41,13 @@ $bf2raw_params.droptop
#if not str($bf2raw_params.dimension_order) == 'keep input order':
--dimension-order $bf2raw_params.dimension_order
#end if
###--overwrite
--debug off &> /dev/null;
--overwrite &> /dev/null;

]]></command>
<inputs>
<section name="io_options" title="Input-output paths" expanded="true">
<param name="input" 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" label="Input image located in Galaxy history"/>
<param name="output_name" type="text" value="output.ome.zarr" label="Output zarr data"/>
<param name="output_name" type="text" value="output.ome.zarr" label="Name of the generated OME-Zarr"/>
</section>
<section name="bf2raw_params" title="Parameters fed to file conversion module">
<conditional name="multiscales" >
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