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annotate bfconvert.xml @ 5:2945efa4cb3d 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 11:55:02 +0000
parents 86e519799f6c
children
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5
2945efa4cb3d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit 4eea5324bf5d02e6ac21006db677dd5a8ecbaaa2
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1 <tool id="ip_convertimage" name="Convert image format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
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2 <description>with Bioformats</description>
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3 <macros>
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4 <import>creators.xml</import>
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5 <import>tests.xml</import>
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6 <token name="@TOOL_VERSION@">6.7.0</token>
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7 <token name="@VERSION_SUFFIX@">4</token>
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8 </macros>
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9 <creator>
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10 <expand macro="creators/alliecreason"/>
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11 <expand macro="creators/bmcv"/>
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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>
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16 <xrefs>
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17 <xref type="biii">python-bioformats</xref>
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18 </xrefs>
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19 <requirements>
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20 <requirement type="package" version="@TOOL_VERSION@">bftools</requirement>
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21 </requirements>
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22 <command>
0
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23 <![CDATA[
5
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24 ln -s '$input_file' 'input.$input_file.ext' &&
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25
0
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26 bfconvert
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27 #if $series_options['extract'] == 'True'
3
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28 -series $series_options.series
0
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29 #end if
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30 #if $timepoint_options['extract'] == 'True'
3
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31 -timepoint $timepoint_options.timepoint
0
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32 #end if
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33 #if $channel_options['extract'] == 'True'
3
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34 -channel $channel_options.channel
0
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35 #end if
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36 #if $z_options['extract'] == 'True'
3
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37 -z $z_options.z
0
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38 #end if
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39 #if $range_options['extract'] == 'True'
3
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40 -range $range_options.range_lower $range_options.range_upper
0
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41 #end if
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42 #if $crop_options['extract'] == 'True'
3
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43 -crop "$crop_options.crop_x,$crop_options.crop_y,$crop_options.crop_width,$crop_options.crop_height"
0
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44 #end if
1
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45 #if $tile_options['extract'] == 'True'
3
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46 -tilex $tile_options.tile_x -tiley $tile_options.tile_y
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47 #end if
4
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48 #if $pyramid_options.generate == 'True' and $out_format not in ['png', 'jpg', 'eps', 'avi']
3
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49 -pyramid-resolutions $pyramid_options.pyramid_resolutions
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50 -pyramid-scale $pyramid_options.pyramid_scale
1
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51 #end if
3
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52 $bigtiff
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53 $noflat
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54 #if $compression != 'False'
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55 -compression $compression
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56 #end if
5
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57 'input.$input_file.ext' './res.$out_format' &&
3
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58 mv './res.$out_format' ./result_image
0
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59 ]]>
5
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60 </command>
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61 <inputs>
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62 <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"/>
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63 <param name="out_format" type="select" label="Output data type">
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64 <option value="tiff" selected="True">TIFF</option>
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65 <option value="png">PNG</option>
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66 <option value="jpg">JPEG</option>
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67 <option value="ome.tiff">OME TIFF</option>
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68 <option value="jp2">JPEG 2000</option>
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69 <option value="eps">EPS</option>
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70 <option value="avi">AVI</option>
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71 </param>
5
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72
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73 <conditional name="series_options">
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74 <param label="Extract series" name="extract" type="select">
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75 <option selected="True" value="False">All series</option>
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76 <option value="True">Extract series</option>
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77 </param>
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78 <when value="False"> </when>
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79 <when value="True">
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80 <param name="series" type="integer" value="0" label="Series id" />
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81 </when>
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82 </conditional>
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83 <conditional name="timepoint_options">
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84 <param name="extract" type="select" label="Extract timepoint">
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85 <option selected="True" value="False">All timepoints</option>
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86 <option value="True">Extract timepoint</option>
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87 </param>
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88 <when value="False"></when>
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89 <when value="True">
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90 <param name="timepoint" type="integer" value="0" label="Timepoint ID" />
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91 </when>
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92 </conditional>
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93 <conditional name="channel_options">
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94 <param name="extract" type="select" label="Extract channel" >
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95 <option selected="True" value="False">All channels</option>
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96 <option value="True">Extract channel</option>
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97 </param>
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98 <when value="False"> </when>
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99 <when value="True">
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100 <param name="channel" type="integer" value="0" label="Channel id" />
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101 </when>
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102 </conditional>
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103 <conditional name="z_options">
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104 <param label="Extract z-slice" name="extract" type="select">
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105 <option selected="True" value="False">All z-slices</option>
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106 <option value="True">Extract z-slice</option>
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107 </param>
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108 <when value="False"> </when>
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109 <when value="True">
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110 <param name="z" type="integer" value="0" label="Z-slice id" />
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111 </when>
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112 </conditional>
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113 <conditional name="range_options">
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114 <param label="Extract range" name="extract" type="select">
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115 <option selected="True" value="False">All images</option>
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116 <option value="True">Extract range by indicess (inclusive)</option>
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117 </param>
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118 <when value="False"> </when>
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119 <when value="True">
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120 <param name="range_lower" type="integer" value="0" label="Lower image id" />
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121 <param name="range_upper" type="integer" value="1" label="Upper image id" />
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122 </when>
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123 </conditional>
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124 <conditional name="crop_options">
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125 <param label="Extract crop" name="extract" type="select">
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126 <option selected="True" value="False">Full image</option>
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127 <option value="True">Extract crop</option>
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128 </param>
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129 <when value="False"> </when>
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130 <when value="True">
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131 <param name="crop_x" type="integer" value="0" label="X" />
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132 <param name="crop_y" type="integer" value="0" label="Y" />
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133 <param name="crop_width" type="integer" value="512" label="Width" />
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134 <param name="crop_height" type="integer" value="512" label="height" />
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135 </when>
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136 </conditional>
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137 <conditional name="tile_options">
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138 <param label="Tile image" name="extract" type="select">
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139 <option selected="True" value="False">No tiling</option>
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140 <option value="True">Tile image</option>
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141 </param>
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142 <when value="False"> </when>
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143 <when value="True">
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144 <param name="tile_x" type="integer" value="512 " label="Tile width" />
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145 <param name="tile_y" type="integer" value="512 " label="Tile height" />
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146 </when>
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147 </conditional>
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148 <conditional name="pyramid_options">
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149 <param label="Pyramid image" name="generate" type="select" help="Pyramids will be generated only if the selected output format supports pyramids (OME TIFF, JPEG 2000)."><!-- see: https://docs.openmicroscopy.org/bio-formats/6.7.0/supported-formats.html -->
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150 <option selected="True" value="True">Generate Pyramid</option>
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151 <option value="False">No Pyramid</option>
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152 </param>
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153 <when value="True">
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154 <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/>
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155 <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" />
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156 </when>
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157 <when value="False" />
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158 </conditional>
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159 <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/>
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160 <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/>
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161 <param label="Compression" name="compression" type="select">
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162 <option selected="True" value="False">No Compression</option>
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163 <option value="LZW">LZW</option>
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164 <option value="JPEG-2000">JPEG-2000</option>
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165 <option value="JPEG-2000 Lossy">JPEG-2000 Lossy</option>
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166 <option value="JPEG">JPEG</option>
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167 <option value="zlib">zlib</option>
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168 </param>
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169 </inputs>
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170 <outputs>
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171 <data format="tiff" name="output" from_work_dir="result_image">
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172 <change_format>
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173 <when input="out_format" value="tiff" format="tiff" />
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174 <when input="out_format" value="png" format="png" />
2945efa4cb3d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit 4eea5324bf5d02e6ac21006db677dd5a8ecbaaa2
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175 <when input="out_format" value="jpg" format="jpg" />
2945efa4cb3d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit 4eea5324bf5d02e6ac21006db677dd5a8ecbaaa2
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176 <when input="out_format" value="ome.tiff" format="ome.tiff" />
2945efa4cb3d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit 4eea5324bf5d02e6ac21006db677dd5a8ecbaaa2
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177 <when input="out_format" value="jp2" format="jpg" />
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178 <when input="out_format" value="eps" format="eps" />
2945efa4cb3d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit 4eea5324bf5d02e6ac21006db677dd5a8ecbaaa2
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179 <when input="out_format" value="avi" format="avi" />
2945efa4cb3d planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit 4eea5324bf5d02e6ac21006db677dd5a8ecbaaa2
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180 </change_format>
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181 </data>
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182 </outputs>
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183 <tests>
0
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184 <test>
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185 <param name="input_file" value="input.png" />
5
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186 <param name="out_format" value="tiff" />
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187 <expand macro="tests/intensity_image_diff" name="output" value="res.tiff" ftype="tiff"/>
0
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188 </test>
3
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189 <test>
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190 <param name="input_file" value="input.png" />
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191 <param name="out_format" value="ome.tiff" />
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192 <conditional name="pyramid_options">
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193 <param name="generate" value="True"/>
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194 <param name="pyramid_resolutions" value="4"/>
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195 <param name="pyramid_scale" value="2"/>
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196 </conditional>
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197 <expand macro="tests/intensity_image_diff" name="output" value="res.ome.tiff" ftype="ome.tiff"/>
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198 </test>
4
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199 <test>
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200 <param name="input_file" value="input.tiff" />
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201 <param name="out_format" value="png" />
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202 <expand macro="tests/intensity_image_diff" name="output" value="input.tiff.png" ftype="png"/>
4
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203 </test>
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204 </tests>
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205 <help>
0
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206
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207 **Converts image format.**
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208
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209 Universial image converter using bioformats.
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210
0
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211 </help>
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212 <citations>
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213 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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214 </citations>
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215 </tool>
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216