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annotate bf2raw.xml @ 2:51d1460d03e6 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit d12bb8de65b311ab1c07b69147388a4bd3d9887a
author imgteam
date Tue, 20 Jan 2026 11:48:35 +0000
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1 <tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.0">
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2 <description>with Bio-Formats</description>
0
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3 <macros>
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4 <import>creators.xml</import>
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5 <token name="@TOOL_VERSION@">0.7.0</token>
2
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6 <token name="@VERSION_SUFFIX@">5</token>
0
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7 </macros>
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8 <creator>
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9 <expand macro="creators/bugraoezdemir"/>
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10 <expand macro="creators/bmcv"/>
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11 <expand macro="creators/kostrykin"/>
0
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12 </creator>
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13 <edam_operations>
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14 <edam_operation>operation_3443</edam_operation>
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15 </edam_operations>
1
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16 <xrefs>
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17 <xref type="bio.tools">bio-formats</xref>
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18 <xref type="biii">bio-formats</xref>
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19 </xrefs>
0
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20 <requirements>
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21 <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container>
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22 </requirements>
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23 <command><![CDATA[
1
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24
2
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25 ## Create final output directory
1
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26 if [ ! -d $output.files_path ]; then
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27 mkdir -p $output.files_path;
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28 fi;
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29
2
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30 ## Use an intermediate output directory if only a subgroup of the Zarr is wanted for export
51d1460d03e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit d12bb8de65b311ab1c07b69147388a4bd3d9887a
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31 #if str($io_options.subgroup) == ''
51d1460d03e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit d12bb8de65b311ab1c07b69147388a4bd3d9887a
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32 ln -s $output.files_path ./output;
51d1460d03e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit d12bb8de65b311ab1c07b69147388a4bd3d9887a
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33 #else
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34 mkdir ./output;
51d1460d03e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit d12bb8de65b311ab1c07b69147388a4bd3d9887a
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35 #end if
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36
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37 ## Input symlink to obscure the dataset directory for reproducible results
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38 ln -s ${io_options.input} ./input;
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39
2
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40 export _JAVA_OPTIONS="-Djava.io.tmpdir=/usr/local/man/" && bioformats2raw ./input ./output/.
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41 #if $bf2raw_params.multiscales['options'] == 'auto':
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42 --target-min-size $bf2raw_params.multiscales.min_xy_size
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43 #elif $bf2raw_params.multiscales['options'] == 'manual':
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44 --resolutions $bf2raw_params.resolutions
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45 #end if
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46 --tile_height $bf2raw_params.tile_height
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47 --tile_width $bf2raw_params.tile_width
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48 --chunk_depth $bf2raw_params.chunk_depth
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49 --downsample-type $bf2raw_params.downsample_type
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50 --compression $bf2raw_params.compression
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51 --max_workers "\${GALAXY_SLOTS:-4}"
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52 $bf2raw_params.nesting
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53 $bf2raw_params.omefolder
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54 $bf2raw_params.droptop
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55 #if not str($bf2raw_params.dimension_order) == 'keep input order':
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56 --dimension-order $bf2raw_params.dimension_order
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57 #end if
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58 --overwrite &> /dev/null;
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59
2
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60 ## Optionally, export a subgroup of the Zarr
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61 #if str($io_options.subgroup) != ''
2
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62 mv "./output/${io_options.subgroup}"/* "./output/${io_options.subgroup}"/.* "${output.files_path}/";
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63 mv "./output/OME" "${output.files_path}/OME";
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64 #end if
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65
0
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66 ]]></command>
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67 <inputs>
1
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68 <section name="io_options" title="Input/Output" expanded="true">
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69 <param name="input" type="data"
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70 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"
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71 label="Input image"/>
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72 <param name="subgroup" type="text" value="" optional="true" label="Select a subgroup"
2
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73 help='Only export a subgroup of the Zarr dataset (e.g., use "&lt;tt&gt;0&lt;/tt&gt;" to only export the &lt;tt&gt;/0&lt;/tt&gt; subgroup of the Zarr). Leave empty to export the full Zarr.'>
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74 <validator type="regex" message="Subgroup name cannot be empty." negate="true">.*//.*</validator>
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75 <validator type="expression" message='Subgroup name must not start with a "/"' negate="true">value.startswith("/")</validator>
51d1460d03e6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit d12bb8de65b311ab1c07b69147388a4bd3d9887a
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76 <validator type="expression" message='Subgroup name must not end with a "/"' negate="true">value.endswith("/")</validator>
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77 </param>
0
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78 </section>
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79 <section name="bf2raw_params" title="Parameters fed to file conversion module">
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80 <conditional name="multiscales" >
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81 <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" >
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82 <option value="auto" selected="true">auto</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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83 <option value="manual" selected="false">manual</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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84 </param>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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85 <when value="auto">
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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86 <param name="min_xy_size" type="integer" min="1" optional="true" label="Min x-y dimension for the lowest resolution" value="256" />
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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87 </when>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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88 <when value="manual">
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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89 <param name="resolution_count" type="integer" min="1" optional="true" label="Number of resolution layers" value="3"/>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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90 </when>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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91 </conditional >
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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92 <param name="tile_height" type="integer" label="Tile height" value="96" min="1" />
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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93 <param name="tile_width" type="integer" label="Tile width" value="96" min="1" />
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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94 <param name="chunk_depth" type="integer" label="Chunk depth" value="1" min="1" />
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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95 <param name="downsample_type" type="select" label="Downsampling method" multiple="false" >
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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96 <option value="SIMPLE" selected="true">SIMPLE</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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97 <option value="GAUSSIAN" selected="false">GAUSSIAN</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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98 <option value="AREA" selected="false">AREA</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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99 <option value="LINEAR" selected="false">LINEAR</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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100 <option value="CUBIC" selected="false">CUBIC</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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101 <option value="LANCZOS" selected="false">LANCZOS</option>
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102 </param>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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103 <param name="compression" type="select" label="Compression method" multiple="false" >
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104 <option value="null" selected="false">null</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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105 <option value="zlib" selected="false">zlib</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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106 <option value="blosc" selected="true">blosc</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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107 </param>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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108 <param name="dimension_order" type="select" label="Dimension order" multiple="false">
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109 <option value="keep input order" selected="true">keep input order</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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110 <option value="XYZCT" selected="false">XYZCT</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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111 <option value="XYZTC" selected="false">XYZTC</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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112 <option value="XYCTZ" selected="false">XYCTZ</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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113 <option value="XYCZT" selected="false">XYCZT</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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114 <option value="XYTCZ" selected="false">XYTCZ</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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115 <option value="XYTZC" selected="false">XYTZC</option>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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116 </param>
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117 <param name="nesting" type="boolean" label="Use ' / ' as chunk path separator" truevalue="" falsevalue="--no-nested" checked="true" />
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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118 <param name="omefolder" type="boolean" label="Export OME metadata" truevalue="" falsevalue="--no-ome-meta-export" checked="true" />
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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119 <param name="droptop" type="boolean" label="Drop the series layer in the OME-Zarr folder hierarchy" truevalue="--scale-format-string '%2$d'" falsevalue="" checked="false" />
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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120 </section>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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121 </inputs>
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122 <outputs>
1
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123 <data name="output" format="zarr"/>
0
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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124 </outputs>
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125 <tests>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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126 <test expect_num_outputs="1">
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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127 <section name="io_options">
1
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128 <param name="input" value="xyz_8bit__mitotic_plate_calibrated.tiff"/>
0
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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129 </section>
1
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130 <output name="output" ftype="zarr">
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131 <extra_files type="file" name=".zattrs" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs"/>
21fedce225f6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 86cf7f811cdfe5ffcc578603f51900c263e7ecd5
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132 <extra_files type="file" name=".zgroup" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zgroup"/>
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133 <extra_files type="file" name="OME/METADATA.ome.xml" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr/OME/METADATA.ome.xml"/>
0
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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134 </output>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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135 </test>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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136 <test expect_num_outputs="1">
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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137 <section name="io_options">
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138 <param name="input" value="coins.png"/>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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139 </section>
1
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140 <output name="output" ftype="zarr">
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141 <extra_files type="file" name=".zattrs" value="coins.ome.zarr/.zattrs"/>
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142 <extra_files type="file" name=".zgroup" value="coins.ome.zarr/.zgroup"/>
21fedce225f6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 86cf7f811cdfe5ffcc578603f51900c263e7ecd5
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143 <extra_files type="file" name="OME/METADATA.ome.xml" value="coins.ome.zarr/OME/METADATA.ome.xml"/>
0
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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144 </output>
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145 </test>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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146 <test expect_num_outputs="1">
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147 <section name="io_options">
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148 <param name="input" value="camera.jpg"/>
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149 </section>
1
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150 <output name="output" ftype="zarr">
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151 <extra_files type="file" name=".zattrs" value="camera.ome.zarr/.zattrs"/>
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152 <extra_files type="file" name=".zgroup" value="camera.ome.zarr/.zgroup"/>
21fedce225f6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 86cf7f811cdfe5ffcc578603f51900c263e7ecd5
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153 <extra_files type="file" name="OME/METADATA.ome.xml" value="camera.ome.zarr/OME/METADATA.ome.xml"/>
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154 </output>
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155 </test>
21fedce225f6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 86cf7f811cdfe5ffcc578603f51900c263e7ecd5
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156 <test expect_num_outputs="1">
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157 <section name="io_options">
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158 <param name="input" value="coins.png"/>
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159 <param name="subgroup" value="0"/>
21fedce225f6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 86cf7f811cdfe5ffcc578603f51900c263e7ecd5
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160 </section>
21fedce225f6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 86cf7f811cdfe5ffcc578603f51900c263e7ecd5
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161 <output name="output" ftype="zarr">
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162 <extra_files type="file" name=".zattrs" value="coins.ome.zarr/0/.zattrs"/>
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163 <extra_files type="file" name=".zgroup" value="coins.ome.zarr/0/.zgroup"/>
21fedce225f6 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 86cf7f811cdfe5ffcc578603f51900c263e7ecd5
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164 <extra_files type="file" name="OME/METADATA.ome.xml" value="coins.ome.zarr/OME/METADATA.ome.xml"/>
0
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165 </output>
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166 </test>
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167 </tests>
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168 <help>
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169
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170 **Converts images to OME-Zarr.**
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171
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172 Tool based on Bio-Formats that converts a wide range of image file formats to the cloud-optimised format
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173 OME-Zarr following the `OME-NGFF`_ specification.
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174
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175 .. _OME-NGFF: https://ngff.openmicroscopy.org/latest
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176
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177 </help>
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178 <citations>
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179 <citation type="doi">https://doi.org/10.5281/zenodo.5548102 </citation>
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180 </citations>
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181 </tool>