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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
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4:86e519799f6c 5:2945efa4cb3d
1 <tool id="ip_convertimage" name="Convert image" version="6.7.0+galaxy1"> 1 <tool id="ip_convertimage" name="Convert image format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
2 <description>Convert image</description> 2 <description>with Bioformats</description>
3 <requirements> 3 <macros>
4 <requirement type="package" version="6.7.0">bftools</requirement> 4 <import>creators.xml</import>
5 </requirements> 5 <import>tests.xml</import>
6 <command> 6 <token name="@TOOL_VERSION@">6.7.0</token>
7 <token name="@VERSION_SUFFIX@">4</token>
8 </macros>
9 <creator>
10 <expand macro="creators/alliecreason"/>
11 <expand macro="creators/bmcv"/>
12 </creator>
13 <edam_operations>
14 <edam_operation>operation_3443</edam_operation>
15 </edam_operations>
16 <xrefs>
17 <xref type="biii">python-bioformats</xref>
18 </xrefs>
19 <requirements>
20 <requirement type="package" version="@TOOL_VERSION@">bftools</requirement>
21 </requirements>
22 <command>
7 <![CDATA[ 23 <![CDATA[
24 ln -s '$input_file' 'input.$input_file.ext' &&
25
8 bfconvert 26 bfconvert
9 #if $series_options['extract'] == 'True' 27 #if $series_options['extract'] == 'True'
10 -series $series_options.series 28 -series $series_options.series
11 #end if 29 #end if
12 #if $timepoint_options['extract'] == 'True' 30 #if $timepoint_options['extract'] == 'True'
34 $bigtiff 52 $bigtiff
35 $noflat 53 $noflat
36 #if $compression != 'False' 54 #if $compression != 'False'
37 -compression $compression 55 -compression $compression
38 #end if 56 #end if
39 '$input_file' './res.$out_format' && 57 'input.$input_file.ext' './res.$out_format' &&
40 mv './res.$out_format' ./result_image 58 mv './res.$out_format' ./result_image
41 ]]> 59 ]]>
42 </command> 60 </command>
43 <inputs> 61 <inputs>
44 <param label="Input Image" name="input_file" 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"/> 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"/>
45 <param name="out_format" type="select" label="Output data type"> 63 <param name="out_format" type="select" label="Output data type">
46 <option value="tiff" selected="True">TIFF</option> 64 <option value="tiff" selected="True">TIFF</option>
47 <option value="png">PNG</option> 65 <option value="png">PNG</option>
48 <option value="jpg">JPEG</option> 66 <option value="jpg">JPEG</option>
49 <option value="ome.tiff">OME TIFF</option> 67 <option value="ome.tiff">OME TIFF</option>
50 <option value="jp2">JPEG 2000</option> 68 <option value="jp2">JPEG 2000</option>
51 <option value="eps">EPS</option> 69 <option value="eps">EPS</option>
52 <option value="avi">AVI</option> 70 <option value="avi">AVI</option>
53 </param>
54
55 <conditional name="series_options">
56 <param label="Extract series" name="extract" type="select">
57 <option selected="True" value="False">All series</option>
58 <option value="True">Extract series</option>
59 </param> 71 </param>
60 <when value="False"> </when> 72
61 <when value="True"> 73 <conditional name="series_options">
62 <param name="series" type="integer" value="0" label="Series id" /> 74 <param label="Extract series" name="extract" type="select">
63 </when> 75 <option selected="True" value="False">All series</option>
64 </conditional> 76 <option value="True">Extract series</option>
65 <conditional name="timepoint_options"> 77 </param>
66 <param name="extract" type="select" label="Extract timepoint"> 78 <when value="False"> </when>
67 <option selected="True" value="False">All timepoints</option> 79 <when value="True">
68 <option value="True">Extract timepoint</option> 80 <param name="series" type="integer" value="0" label="Series id" />
69 </param> 81 </when>
70 <when value="False"></when> 82 </conditional>
71 <when value="True"> 83 <conditional name="timepoint_options">
72 <param name="timepoint" type="integer" value="0" label="Timepoint ID" /> 84 <param name="extract" type="select" label="Extract timepoint">
73 </when> 85 <option selected="True" value="False">All timepoints</option>
74 </conditional> 86 <option value="True">Extract timepoint</option>
75 <conditional name="channel_options"> 87 </param>
76 <param name="extract" type="select" label="Extract channel" > 88 <when value="False"></when>
77 <option selected="True" value="False">All channels</option> 89 <when value="True">
78 <option value="True">Extract channel</option> 90 <param name="timepoint" type="integer" value="0" label="Timepoint ID" />
79 </param> 91 </when>
80 <when value="False"> </when> 92 </conditional>
81 <when value="True"> 93 <conditional name="channel_options">
82 <param name="channel" type="integer" value="0" label="Channel id" /> 94 <param name="extract" type="select" label="Extract channel" >
83 </when> 95 <option selected="True" value="False">All channels</option>
84 </conditional> 96 <option value="True">Extract channel</option>
85 <conditional name="z_options"> 97 </param>
86 <param label="Extract z-slice" name="extract" type="select"> 98 <when value="False"> </when>
87 <option selected="True" value="False">All z-slices</option> 99 <when value="True">
88 <option value="True">Extract z-slice</option> 100 <param name="channel" type="integer" value="0" label="Channel id" />
89 </param> 101 </when>
90 <when value="False"> </when> 102 </conditional>
91 <when value="True"> 103 <conditional name="z_options">
92 <param name="z" type="integer" value="0" label="Z-slice id" /> 104 <param label="Extract z-slice" name="extract" type="select">
93 </when> 105 <option selected="True" value="False">All z-slices</option>
94 </conditional> 106 <option value="True">Extract z-slice</option>
95 <conditional name="range_options"> 107 </param>
96 <param label="Extract range" name="extract" type="select"> 108 <when value="False"> </when>
97 <option selected="True" value="False">All images</option> 109 <when value="True">
98 <option value="True">Extract range by indicess (inclusive)</option> 110 <param name="z" type="integer" value="0" label="Z-slice id" />
99 </param> 111 </when>
100 <when value="False"> </when> 112 </conditional>
101 <when value="True"> 113 <conditional name="range_options">
102 <param name="range_lower" type="integer" value="0" label="Lower image id" /> 114 <param label="Extract range" name="extract" type="select">
103 <param name="range_upper" type="integer" value="1" label="Upper image id" /> 115 <option selected="True" value="False">All images</option>
104 </when> 116 <option value="True">Extract range by indicess (inclusive)</option>
105 </conditional> 117 </param>
106 <conditional name="crop_options"> 118 <when value="False"> </when>
107 <param label="Extract crop" name="extract" type="select"> 119 <when value="True">
108 <option selected="True" value="False">Full image</option> 120 <param name="range_lower" type="integer" value="0" label="Lower image id" />
109 <option value="True">Extract crop</option> 121 <param name="range_upper" type="integer" value="1" label="Upper image id" />
110 </param> 122 </when>
111 <when value="False"> </when> 123 </conditional>
112 <when value="True"> 124 <conditional name="crop_options">
113 <param name="crop_x" type="integer" value="0" label="X" /> 125 <param label="Extract crop" name="extract" type="select">
114 <param name="crop_y" type="integer" value="0" label="Y" /> 126 <option selected="True" value="False">Full image</option>
115 <param name="crop_width" type="integer" value="512" label="Width" /> 127 <option value="True">Extract crop</option>
116 <param name="crop_height" type="integer" value="512" label="height" /> 128 </param>
117 </when> 129 <when value="False"> </when>
118 </conditional> 130 <when value="True">
119 <conditional name="tile_options"> 131 <param name="crop_x" type="integer" value="0" label="X" />
120 <param label="Tile image" name="extract" type="select"> 132 <param name="crop_y" type="integer" value="0" label="Y" />
121 <option selected="True" value="False">No tiling</option> 133 <param name="crop_width" type="integer" value="512" label="Width" />
122 <option value="True">Tile image</option> 134 <param name="crop_height" type="integer" value="512" label="height" />
123 </param> 135 </when>
124 <when value="False"> </when> 136 </conditional>
125 <when value="True"> 137 <conditional name="tile_options">
126 <param name="tile_x" type="integer" value="512 " label="Tile width" /> 138 <param label="Tile image" name="extract" type="select">
127 <param name="tile_y" type="integer" value="512 " label="Tile height" /> 139 <option selected="True" value="False">No tiling</option>
128 </when> 140 <option value="True">Tile image</option>
129 </conditional> 141 </param>
130 <conditional name="pyramid_options"> 142 <when value="False"> </when>
131 <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 --> 143 <when value="True">
132 <option selected="True" value="True">Generate Pyramid</option> 144 <param name="tile_x" type="integer" value="512 " label="Tile width" />
133 <option value="False">No Pyramid</option> 145 <param name="tile_y" type="integer" value="512 " label="Tile height" />
134 </param> 146 </when>
135 <when value="True"> 147 </conditional>
136 <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/> 148 <conditional name="pyramid_options">
137 <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" /> 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 -->
138 </when> 150 <option selected="True" value="True">Generate Pyramid</option>
139 <when value="False" /> 151 <option value="False">No Pyramid</option>
140 </conditional> 152 </param>
141 <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/> 153 <when value="True">
142 <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/> 154 <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/>
143 <param label="Compression" name="compression" type="select"> 155 <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" />
144 <option selected="True" value="False">No Compression</option> 156 </when>
145 <option value="LZW">LZW</option> 157 <when value="False" />
146 <option value="JPEG-2000">JPEG-2000</option> 158 </conditional>
147 <option value="JPEG-2000 Lossy">JPEG-2000 Lossy</option> 159 <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/>
148 <option value="JPEG">JPEG</option> 160 <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/>
149 <option value="zlib">zlib</option> 161 <param label="Compression" name="compression" type="select">
150 </param> 162 <option selected="True" value="False">No Compression</option>
151 </inputs> 163 <option value="LZW">LZW</option>
152 <outputs> 164 <option value="JPEG-2000">JPEG-2000</option>
153 <data format="tiff" name="output" from_work_dir="result_image"> 165 <option value="JPEG-2000 Lossy">JPEG-2000 Lossy</option>
154 <change_format> 166 <option value="JPEG">JPEG</option>
155 <when input="out_format" value="tiff" format="tiff" /> 167 <option value="zlib">zlib</option>
156 <when input="out_format" value="png" format="png" /> 168 </param>
157 <when input="out_format" value="jpg" format="jpg" /> 169 </inputs>
158 <when input="out_format" value="ome.tiff" format="ome.tiff" /> 170 <outputs>
159 <when input="out_format" value="jp2" format="jpg" /> 171 <data format="tiff" name="output" from_work_dir="result_image">
160 <when input="out_format" value="eps" format="eps" /> 172 <change_format>
161 <when input="out_format" value="avi" format="avi" /> 173 <when input="out_format" value="tiff" format="tiff" />
162 </change_format> 174 <when input="out_format" value="png" format="png" />
163 </data> 175 <when input="out_format" value="jpg" format="jpg" />
164 </outputs> 176 <when input="out_format" value="ome.tiff" format="ome.tiff" />
165 <tests> 177 <when input="out_format" value="jp2" format="jpg" />
178 <when input="out_format" value="eps" format="eps" />
179 <when input="out_format" value="avi" format="avi" />
180 </change_format>
181 </data>
182 </outputs>
183 <tests>
166 <test> 184 <test>
167 <param name="input_file" value="input.png" /> 185 <param name="input_file" value="input.png" />
168 <param name="out_format" value="tiff" /> 186 <param name="out_format" value="tiff" />
169 <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/> 187 <expand macro="tests/intensity_image_diff" name="output" value="res.tiff" ftype="tiff"/>
170 </test> 188 </test>
171 <test> 189 <test>
172 <param name="input_file" value="input.png" /> 190 <param name="input_file" value="input.png" />
173 <param name="out_format" value="ome.tiff" /> 191 <param name="out_format" value="ome.tiff" />
174 <conditional name="pyramid_options"> 192 <conditional name="pyramid_options">
175 <param name="generate" value="True"/> 193 <param name="generate" value="True"/>
176 <param name="pyramid_resolutions" value="4"/> 194 <param name="pyramid_resolutions" value="4"/>
177 <param name="pyramid_scale" value="2"/> 195 <param name="pyramid_scale" value="2"/>
178 </conditional> 196 </conditional>
179 <output name="output" value="res.ome.tiff" ftype="ome.tiff" compare="sim_size"/> 197 <expand macro="tests/intensity_image_diff" name="output" value="res.ome.tiff" ftype="ome.tiff"/>
180 </test> 198 </test>
181 <test> 199 <test>
182 <param name="input_file" value="input.tiff" /> 200 <param name="input_file" value="input.tiff" />
183 <param name="out_format" value="png" /> 201 <param name="out_format" value="png" />
184 <output name="output" value="input.tiff.png" ftype="png" compare="sim_size"/> 202 <expand macro="tests/intensity_image_diff" name="output" value="input.tiff.png" ftype="png"/>
185 </test> 203 </test>
186 </tests> 204 </tests>
187 <help> 205 <help>
188 **What it does** 206
189 207 **Converts image format.**
190 Universial image converter using bioformats. 208
209 Universial image converter using bioformats.
210
191 </help> 211 </help>
192 <citations> 212 <citations>
193 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> 213 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
194 </citations> 214 </citations>
195 </tool> 215 </tool>