Mercurial > repos > imgteam > bioformats2raw
changeset 6:51ff1667c499 draft default tip
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit d12bb8de65b311ab1c07b69147388a4bd3d9887a
| author | imgteam |
|---|---|
| date | Tue, 20 Jan 2026 11:49:57 +0000 |
| parents | d028dc14532e |
| children | |
| files | bf2raw.xml |
| diffstat | 1 files changed, 19 insertions(+), 7 deletions(-) [+] |
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--- a/bf2raw.xml Mon Jan 19 19:43:30 2026 +0000 +++ b/bf2raw.xml Tue Jan 20 11:49:57 2026 +0000 @@ -3,7 +3,7 @@ <macros> <import>creators.xml</import> <token name="@TOOL_VERSION@">0.7.0</token> - <token name="@VERSION_SUFFIX@">4</token> + <token name="@VERSION_SUFFIX@">5</token> </macros> <creator> <expand macro="creators/bugraoezdemir"/> @@ -22,13 +22,22 @@ </requirements> <command><![CDATA[ +## Create final output directory if [ ! -d $output.files_path ]; then mkdir -p $output.files_path; fi; +## Use an intermediate output directory if only a subgroup of the Zarr is wanted for export +#if str($io_options.subgroup) == '' + ln -s $output.files_path ./output; +#else + mkdir ./output; +#end if + +## Input symlink to obscure the dataset directory for reproducible results ln -s ${io_options.input} ./input; -export _JAVA_OPTIONS="-Djava.io.tmpdir=/usr/local/man/" && bioformats2raw ./input $output.files_path +export _JAVA_OPTIONS="-Djava.io.tmpdir=/usr/local/man/" && bioformats2raw ./input ./output/. #if $bf2raw_params.multiscales['options'] == 'auto': --target-min-size $bf2raw_params.multiscales.min_xy_size #elif $bf2raw_params.multiscales['options'] == 'manual': @@ -48,11 +57,10 @@ #end if --overwrite &> /dev/null; +## Optionally, export a subgroup of the Zarr #if str($io_options.subgroup) != '' - mv ${output.files_path}/${io_options.subgroup} ./subdir; - mv ${output.files_path}/OME ./subdir/OME; - rm -rf ${output.files_path}; - mv ./subdir ${output.files_path}; + mv "./output/${io_options.subgroup}"/* "./output/${io_options.subgroup}"/.* "${output.files_path}/"; + mv "./output/OME" "${output.files_path}/OME"; #end if ]]></command> @@ -62,7 +70,11 @@ format="scn,ndpi,tf8,vms,xml,pcx,binary,hdr,mov,psd,pbm,nrrd,tiff,pgm,ppm,txt,tf2,zip,top,gif,wav,btf,bmp,png,gz,cif,fli,btf,jpg,avi,html,sif,csv,ome.tiff,par,fits,jp2,eps,nhdr,svs,mrc" label="Input image"/> <param name="subgroup" type="text" value="" optional="true" label="Select a subgroup" - help='Only export a subgroup of the Zarr dataset (e.g., use "<tt>0</tt>" to only export the <tt>/0</tt> subgroup of the Zarr). Leave empty to export the full Zarr.'/> + help='Only export a subgroup of the Zarr dataset (e.g., use "<tt>0</tt>" to only export the <tt>/0</tt> subgroup of the Zarr). Leave empty to export the full Zarr.'> + <validator type="regex" message="Subgroup name cannot be empty." negate="true">.*//.*</validator> + <validator type="expression" message='Subgroup name must not start with a "/"' negate="true">value.startswith("/")</validator> + <validator type="expression" message='Subgroup name must not end with a "/"' negate="true">value.endswith("/")</validator> + </param> </section> <section name="bf2raw_params" title="Parameters fed to file conversion module"> <conditional name="multiscales" >