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annotate bf2raw.xml @ 0:31fee86b0b75 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
author imgteam
date Wed, 17 Dec 2025 11:22:22 +0000
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31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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1 <tool id="bf2raw" name="Convert to OME-Zarr" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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2 <description>with Bioformats</description>
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3 <macros>
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4 <import>creators.xml</import>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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5 <token name="@TOOL_VERSION@">0.7.0</token>
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6 <token name="@VERSION_SUFFIX@">3</token>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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7 </macros>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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8 <creator>
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9 <expand macro="creators/bugraoezdemir"/>
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10 </creator>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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11 <edam_operations>
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12 <edam_operation>operation_3443</edam_operation>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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13 </edam_operations>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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14 <requirements>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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15 <container type="docker">quay.io/biocontainers/mulled-v2-ea5a9ffc5f22f92a78f0cd24aac43eb503c0e523:4c010c399f61cde74da64343581999ada3e11e24-0</container>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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16 </requirements>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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17 <command><![CDATA[
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18 if [ ! -d $output.files_path ];then
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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19 mkdir -p $output.files_path;
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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20 fi;
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21
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22 #if str($io_options.input.ext)=='html':
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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23 #set dirlist=os.listdir($io_options.input.files_path)
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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24 #assert len($dirlist) > 0
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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25 #set input_path=os.path.join(str($io_options.input.files_path), str($dirlist[0]))
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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26 #else:
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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27 #set input_path=$io_options.input
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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28 #end if
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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29
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30 export _JAVA_OPTIONS="-Djava.io.tmpdir=/usr/local/man/" && bioformats2raw $input_path $output.files_path/$io_options.output_name
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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31 #if $bf2raw_params.multiscales['options'] == 'auto':
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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32 --target-min-size $bf2raw_params.multiscales.min_xy_size
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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33 #elif $bf2raw_params.multiscales['options'] == 'manual':
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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34 --resolutions $bf2raw_params.resolutions
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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35 #end if
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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36 --tile_height $bf2raw_params.tile_height
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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37 --tile_width $bf2raw_params.tile_width
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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38 --chunk_depth $bf2raw_params.chunk_depth
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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39 --downsample-type $bf2raw_params.downsample_type
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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40 --compression $bf2raw_params.compression
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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41 --max_workers "\${GALAXY_SLOTS:-4}"
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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42 $bf2raw_params.nesting
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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43 $bf2raw_params.omefolder
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44 $bf2raw_params.droptop
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45 #if not str($bf2raw_params.dimension_order) == 'keep input order':
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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46 --dimension-order $bf2raw_params.dimension_order
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47 #end if
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48 --overwrite &> /dev/null;
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49
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50 ]]></command>
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51 <inputs>
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52 <section name="io_options" title="Input-output paths" expanded="true">
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53 <param name="input" type="data" 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 located in Galaxy history"/>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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54 <param name="output_name" type="text" value="output.ome.zarr" label="Name of the generated OME-Zarr"/>
31fee86b0b75 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bioformats2raw commit 8e99ddb62ceab1da15996906a0813826b62d38fe
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55 </section>
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56 <section name="bf2raw_params" title="Parameters fed to file conversion module">
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57 <conditional name="multiscales" >
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58 <param name="options" type="select" multiple="false" label="How should the number of resolutions be determined?" >
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59 <option value="auto" selected="true">auto</option>
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60 <option value="manual" selected="false">manual</option>
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61 </param>
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62 <when value="auto">
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63 <param name="min_xy_size" type="integer" min="1" optional="true" label="Min x-y dimension for the lowest resolution" value="256" />
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64 </when>
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65 <when value="manual">
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66 <param name="resolution_count" type="integer" min="1" optional="true" label="Number of resolution layers" value="3"/>
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67 </when>
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68 </conditional >
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69 <param name="tile_height" type="integer" label="Tile height" value="96" min="1" />
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70 <param name="tile_width" type="integer" label="Tile width" value="96" min="1" />
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71 <param name="chunk_depth" type="integer" label="Chunk depth" value="1" min="1" />
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72 <param name="downsample_type" type="select" label="Downsampling method" multiple="false" >
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73 <option value="SIMPLE" selected="true">SIMPLE</option>
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74 <option value="GAUSSIAN" selected="false">GAUSSIAN</option>
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75 <option value="AREA" selected="false">AREA</option>
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76 <option value="LINEAR" selected="false">LINEAR</option>
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77 <option value="CUBIC" selected="false">CUBIC</option>
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78 <option value="LANCZOS" selected="false">LANCZOS</option>
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79 </param>
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80 <param name="compression" type="select" label="Compression method" multiple="false" >
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81 <option value="null" selected="false">null</option>
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82 <option value="zlib" selected="false">zlib</option>
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83 <option value="blosc" selected="true">blosc</option>
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84 </param>
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85 <param name="dimension_order" type="select" label="Dimension order" multiple="false">
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86 <option value="keep input order" selected="true">keep input order</option>
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87 <option value="XYZCT" selected="false">XYZCT</option>
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88 <option value="XYZTC" selected="false">XYZTC</option>
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89 <option value="XYCTZ" selected="false">XYCTZ</option>
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90 <option value="XYCZT" selected="false">XYCZT</option>
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91 <option value="XYTCZ" selected="false">XYTCZ</option>
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92 <option value="XYTZC" selected="false">XYTZC</option>
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93 </param>
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94 <param name="nesting" type="boolean" label="Use ' / ' as chunk path separator" truevalue="" falsevalue="--no-nested" checked="true" />
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95 <param name="omefolder" type="boolean" label="Export OME metadata" truevalue="" falsevalue="--no-ome-meta-export" checked="true" />
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96 <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" />
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97 </section>
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98 </inputs>
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99 <outputs>
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100 <data name="output" format="html" label="OME-Zarr Output" />
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101 </outputs>
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102 <tests>
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103 <test expect_num_outputs="1">
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104 <section name="io_options">
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105 <param name="input" value="xyz_8bit__mitotic_plate_calibrated.tif"/>
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106 <param name="output_name" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr" />
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107 </section>
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108 <output name="output" ftype="html">
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109 <extra_files type="file" name="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" value="xyz_8bit__mitotic_plate_calibrated.ome.zarr/.zattrs" />
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110 </output>
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111 </test>
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112 <test expect_num_outputs="1">
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113 <section name="io_options">
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114 <param name="input" value="coins.png"/>
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115 <param name="output_name" value="coins.ome.zarr" />
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116 </section>
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117 <output name="output" ftype="html">
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118 <extra_files type="file" name="coins.ome.zarr/.zgroup" value="coins.ome.zarr/.zgroup" />
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119 </output>
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120 </test>
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121 <test expect_num_outputs="1">
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122 <section name="io_options">
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123 <param name="input" value="camera.jpg"/>
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124 <param name="output_name" value="camera.ome.zarr" />
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125 </section>
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126 <output name="output" ftype="html">
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127 <extra_files type="file" name="camera.ome.zarr/.zattrs" value="camera.ome.zarr/.zattrs" />
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128 </output>
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129 </test>
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130 </tests>
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131 <help>
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132
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133 **Converts images to OME-Zarr.**
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134
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135 Bioformats-based tool that converts a wide range of image file formats to the cloud-optimised format
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136 OME-Zarr following the `OME-NGFF`_ specification.
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137
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138 .. _OME-NGFF: https://ngff.openmicroscopy.org/latest
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139
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140 </help>
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141 <citations>
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142 <citation type="doi">https://doi.org/10.5281/zenodo.5548102 </citation>
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143 </citations>
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144 </tool>