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comparison bfconvert.xml @ 3:802a235f1ad0 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 1ac9c3e967f78c0001833a4c4d7e877f234d4785
author imgteam
date Thu, 15 Sep 2022 17:18:34 +0000
parents ba0a5567b446
children 86e519799f6c
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2:ba0a5567b446 3:802a235f1ad0
1 <tool id="ip_convertimage" name="Convert image" version="0.4"> 1 <tool id="ip_convertimage" name="Convert image" version="6.7.0+galaxy0">
2 <description>Convert image</description> 2 <description>Convert image</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="5.7.1">bftools</requirement> 4 <requirement type="package" version="6.7.0">bftools</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
7 <![CDATA[ 7 <![CDATA[
8 bfconvert 8 bfconvert
9 #if $series_options['extract'] == 'True' 9 #if $series_options['extract'] == 'True'
10 -series $series 10 -series $series_options.series
11 #end if 11 #end if
12 #if $timepoint_options['extract'] == 'True' 12 #if $timepoint_options['extract'] == 'True'
13 -timepoint $timepoint 13 -timepoint $timepoint_options.timepoint
14 #end if 14 #end if
15 #if $channel_options['extract'] == 'True' 15 #if $channel_options['extract'] == 'True'
16 -channel $channel 16 -channel $channel_options.channel
17 #end if 17 #end if
18 #if $z_options['extract'] == 'True' 18 #if $z_options['extract'] == 'True'
19 -z $z 19 -z $z_options.z
20 #end if 20 #end if
21 #if $range_options['extract'] == 'True' 21 #if $range_options['extract'] == 'True'
22 -range $range_lower $range_upper 22 -range $range_options.range_lower $range_options.range_upper
23 #end if 23 #end if
24 #if $crop_options['extract'] == 'True' 24 #if $crop_options['extract'] == 'True'
25 -crop $crop_x $crop_y $crop_width $crop_height 25 -crop "$crop_options.crop_x,$crop_options.crop_y,$crop_options.crop_width,$crop_options.crop_height"
26 #end if 26 #end if
27 #if $tile_options['extract'] == 'True' 27 #if $tile_options['extract'] == 'True'
28 -tilex $tile_x -tiley $tile_y 28 -tilex $tile_options.tile_x -tiley $tile_options.tile_y
29 #end if 29 #end if
30 '$input_file' ./res.$out_format && 30 #if $pyramid_options.generate == 'True'
31 mv ./res.$out_format ./result_image 31 -pyramid-resolutions $pyramid_options.pyramid_resolutions
32 -pyramid-scale $pyramid_options.pyramid_scale
33 #end if
34 $bigtiff
35 $noflat
36 #if $compression != 'False'
37 -compression $compression
38 #end if
39 '$input_file' './res.$out_format' &&
40 mv './res.$out_format' ./result_image
32 ]]> 41 ]]>
33 </command> 42 </command>
34 <inputs> 43 <inputs>
35 <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"/> 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"/>
36 <param name="out_format" type="select" label="Output data type"> 45 <param name="out_format" type="select" label="Output data type">
37 <option value="tiff" selected="True">TIFF</option> 46 <option value="tiff" selected="True">TIFF</option>
38 <option value="png">PNG</option> 47 <option value="png">PNG</option>
39 <option value="jpg">JPEG</option> 48 <option value="jpg">JPEG</option>
40 <option value="ome.tiff">OME TIFF</option> 49 <option value="ome.tiff">OME TIFF</option>
41 <option value="jp2">JPEG 2000</option> 50 <option value="jp2">JPEG 2000</option>
42 <option value="eps">EPS</option> 51 <option value="eps">EPS</option>
43 <option value="avi">AVI</option> 52 <option value="avi">AVI</option>
44 </param> 53 </param>
45 54
46 <conditional name="series_options"> 55 <conditional name="series_options">
47 <param label="Extract series" name="extract" type="select"> 56 <param label="Extract series" name="extract" type="select">
48 <option selected="True" value="False">All series</option> 57 <option selected="True" value="False">All series</option>
49 <option value="True">Extract series</option> 58 <option value="True">Extract series</option>
50 </param> 59 </param>
51 <when value="False"> </when> 60 <when value="False"> </when>
52 <when value="True"> 61 <when value="True">
53 <param name="series" type="integer" value="0" label="Series id" /> 62 <param name="series" type="integer" value="0" label="Series id" />
54 </when> 63 </when>
55 </conditional> 64 </conditional>
56 <conditional name="timepoint_options"> 65 <conditional name="timepoint_options">
57 <param label="Extract timepoint" name="extract" type="select"> 66 <param name="extract" type="select" label="Extract timepoint">
58 <option selected="True" value="False">All timepoints</option> 67 <option selected="True" value="False">All timepoints</option>
59 <option value="True">Extract timepoint</option> 68 <option value="True">Extract timepoint</option>
60 </param> 69 </param>
61 <when value="False"> </when> 70 <when value="False"></when>
62 <when value="True"> 71 <when value="True">
63 <param name="timepoint" type="integer" value="0" label="Timepoint id" /> 72 <param name="timepoint" type="integer" value="0" label="Timepoint ID" />
64 </when> 73 </when>
65 </conditional> 74 </conditional>
66 <conditional name="channel_options"> 75 <conditional name="channel_options">
67 <param label="Extract channel" name="extract" type="select"> 76 <param name="extract" type="select" label="Extract channel" >
68 <option selected="True" value="False">All channels</option> 77 <option selected="True" value="False">All channels</option>
69 <option value="True">Extract channel</option> 78 <option value="True">Extract channel</option>
70 </param> 79 </param>
71 <when value="False"> </when> 80 <when value="False"> </when>
72 <when value="True"> 81 <when value="True">
73 <param name="channel" type="integer" value="0" label="Channel id" /> 82 <param name="channel" type="integer" value="0" label="Channel id" />
74 </when> 83 </when>
75 </conditional> 84 </conditional>
76 <conditional name="z_options"> 85 <conditional name="z_options">
77 <param label="Extract z-slice" name="extract" type="select"> 86 <param label="Extract z-slice" name="extract" type="select">
78 <option selected="True" value="False">All z-slices</option> 87 <option selected="True" value="False">All z-slices</option>
79 <option value="True">Extract z-slice</option> 88 <option value="True">Extract z-slice</option>
80 </param> 89 </param>
81 <when value="False"> </when> 90 <when value="False"> </when>
82 <when value="True"> 91 <when value="True">
83 <param name="z" type="integer" value="0" label="Z-slice id" /> 92 <param name="z" type="integer" value="0" label="Z-slice id" />
84 </when> 93 </when>
85 </conditional> 94 </conditional>
86 <conditional name="range_options"> 95 <conditional name="range_options">
87 <param label="Extract range" name="extract" type="select"> 96 <param label="Extract range" name="extract" type="select">
88 <option selected="True" value="False">All images</option> 97 <option selected="True" value="False">All images</option>
89 <option value="True">Extract range by indicess (inclusive)</option> 98 <option value="True">Extract range by indicess (inclusive)</option>
90 </param> 99 </param>
91 <when value="False"> </when> 100 <when value="False"> </when>
92 <when value="True"> 101 <when value="True">
93 <param name="range_lower" type="integer" value="0" label="Lower image id" /> 102 <param name="range_lower" type="integer" value="0" label="Lower image id" />
94 <param name="range_upper" type="integer" value="1" label="Upper image id" /> 103 <param name="range_upper" type="integer" value="1" label="Upper image id" />
95 </when> 104 </when>
96 </conditional> 105 </conditional>
97 <conditional name="crop_options"> 106 <conditional name="crop_options">
98 <param label="Extract crop" name="extract" type="select"> 107 <param label="Extract crop" name="extract" type="select">
99 <option selected="True" value="False">Full image</option> 108 <option selected="True" value="False">Full image</option>
100 <option value="True">Extract crop</option> 109 <option value="True">Extract crop</option>
101 </param> 110 </param>
102 <when value="False"> </when> 111 <when value="False"> </when>
103 <when value="True"> 112 <when value="True">
104 <param name="crop_x" type="integer" value="0" label="X" /> 113 <param name="crop_x" type="integer" value="0" label="X" />
105 <param name="crop_y" type="integer" value="0" label="Y" /> 114 <param name="crop_y" type="integer" value="0" label="Y" />
106 <param name="crop_width" type="integer" value="512" label="Width" /> 115 <param name="crop_width" type="integer" value="512" label="Width" />
107 <param name="crop_height" type="integer" value="512" label="height" /> 116 <param name="crop_height" type="integer" value="512" label="height" />
108 </when> 117 </when>
109 </conditional> 118 </conditional>
110 <conditional name="tile_options"> 119 <conditional name="tile_options">
111 <param label="Tile image" name="extract" type="select"> 120 <param label="Tile image" name="extract" type="select">
112 <option selected="True" value="False">No tiling</option> 121 <option selected="True" value="False">No tiling</option>
113 <option value="True">Tile image</option> 122 <option value="True">Tile image</option>
114 </param> 123 </param>
115 <when value="False"> </when> 124 <when value="False"> </when>
116 <when value="True"> 125 <when value="True">
117 <param name="tile_x" type="integer" value="512 " label="Tile width" /> 126 <param name="tile_x" type="integer" value="512 " label="Tile width" />
118 <param name="tile_y" type="integer" value="512 " label="Tile height" /> 127 <param name="tile_y" type="integer" value="512 " label="Tile height" />
119 </when> 128 </when>
120 </conditional> 129 </conditional>
130 <conditional name="pyramid_options">
131 <param label="Pyramid image" name="generate" type="select">
132 <option selected="True" value="True">Generate Pyramid</option>
133 <option value="False">No Pyramid</option>
134 </param>
135 <when value="True">
136 <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/>
137 <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" />
138 </when>
139 </conditional>
140 <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/>
141 <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/>
142 <param label="Compression" name="compression" type="select">
143 <option selected="True" value="False">No Compression</option>
144 <option value="LZW">LZW</option>
145 <option value="JPEG-2000">JPEG-2000</option>
146 <option value="JPEG-2000 Lossy">JPEG-2000 Lossy</option>
147 <option value="JPEG">JPEG</option>
148 <option value="zlib">zlib</option>
149 </param>
121 </inputs> 150 </inputs>
122 <outputs> 151 <outputs>
123 <data format="tiff" name="output" from_work_dir="result_image"> 152 <data format="tiff" name="output" from_work_dir="result_image">
124 <change_format> 153 <change_format>
125 <when input="out_format" value="tiff" format="tiff" /> 154 <when input="out_format" value="tiff" format="tiff" />
126 <when input="out_format" value="png" format="png" /> 155 <when input="out_format" value="png" format="png" />
127 <when input="out_format" value="jpg" format="jpg" /> 156 <when input="out_format" value="jpg" format="jpg" />
128 <when input="out_format" value="ome.tiff" format="tiff" /> 157 <when input="out_format" value="ome.tiff" format="ome.tiff" />
129 <when input="out_format" value="jp2" format="jpg" /> 158 <when input="out_format" value="jp2" format="jpg" />
130 <when input="out_format" value="eps" format="eps" /> 159 <when input="out_format" value="eps" format="eps" />
131 <when input="out_format" value="avi" format="avi" /> 160 <when input="out_format" value="avi" format="avi" />
132 </change_format> 161 </change_format>
133 </data> 162 </data>
136 <test> 165 <test>
137 <param name="input_file" value="input.png" /> 166 <param name="input_file" value="input.png" />
138 <param name="out_format" value="tiff" /> 167 <param name="out_format" value="tiff" />
139 <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/> 168 <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/>
140 </test> 169 </test>
170 <test>
171 <param name="input_file" value="input.png" />
172 <param name="out_format" value="ome.tiff" />
173 <param name="pyramid_options.generate" value="True"/>
174 <param name="pyramid_options.pyramid_resolutions" value="4"/>
175 <param name="pyramid_options.pyramid_scale" value="2"/>
176 <output name="output" value="res.ome.tiff" ftype="ome.tiff" compare="sim_size"/>
177 </test>
141 </tests> 178 </tests>
142 <help> 179 <help>
143 **What it does** 180 **What it does**
144 181
145 Universial image converter using bioformats. 182 Universial image converter using bioformats.