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annotate bfconvert.xml @ 6:fcadded98e61 draft default tip

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
author imgteam
date Thu, 04 Apr 2024 15:23:54 +0000
parents 85edbb7a436b
children
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6
fcadded98e61 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit c045f067a57e8308308cf6329060c7ccd3fc372f
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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@">3</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[
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24 bfconvert
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25 #if $series_options['extract'] == 'True'
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26 -series $series_options.series
0
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27 #end if
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28 #if $timepoint_options['extract'] == 'True'
3
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29 -timepoint $timepoint_options.timepoint
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30 #end if
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31 #if $channel_options['extract'] == 'True'
3
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32 -channel $channel_options.channel
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33 #end if
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34 #if $z_options['extract'] == 'True'
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35 -z $z_options.z
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36 #end if
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37 #if $range_options['extract'] == 'True'
3
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38 -range $range_options.range_lower $range_options.range_upper
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39 #end if
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40 #if $crop_options['extract'] == 'True'
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41 -crop "$crop_options.crop_x,$crop_options.crop_y,$crop_options.crop_width,$crop_options.crop_height"
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42 #end if
1
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43 #if $tile_options['extract'] == 'True'
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44 -tilex $tile_options.tile_x -tiley $tile_options.tile_y
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45 #end if
4
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46 #if $pyramid_options.generate == 'True' and $out_format not in ['png', 'jpg', 'eps', 'avi']
3
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47 -pyramid-resolutions $pyramid_options.pyramid_resolutions
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48 -pyramid-scale $pyramid_options.pyramid_scale
1
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49 #end if
3
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50 $bigtiff
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51 $noflat
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52 #if $compression != 'False'
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53 -compression $compression
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54 #end if
4
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55 '$input_file' './res.$out_format' &&
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56 mv './res.$out_format' ./result_image
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57 ]]>
6
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58 </command>
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59 <inputs>
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60 <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"/>
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61 <param name="out_format" type="select" label="Output data type">
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62 <option value="tiff" selected="True">TIFF</option>
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63 <option value="png">PNG</option>
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64 <option value="jpg">JPEG</option>
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65 <option value="ome.tiff">OME TIFF</option>
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66 <option value="jp2">JPEG 2000</option>
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67 <option value="eps">EPS</option>
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68 <option value="avi">AVI</option>
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69 </param>
6
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70
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71 <conditional name="series_options">
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72 <param label="Extract series" name="extract" type="select">
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73 <option selected="True" value="False">All series</option>
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74 <option value="True">Extract series</option>
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75 </param>
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76 <when value="False"> </when>
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77 <when value="True">
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78 <param name="series" type="integer" value="0" label="Series id" />
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79 </when>
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80 </conditional>
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81 <conditional name="timepoint_options">
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82 <param name="extract" type="select" label="Extract timepoint">
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83 <option selected="True" value="False">All timepoints</option>
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84 <option value="True">Extract timepoint</option>
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85 </param>
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86 <when value="False"></when>
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87 <when value="True">
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88 <param name="timepoint" type="integer" value="0" label="Timepoint ID" />
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89 </when>
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90 </conditional>
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91 <conditional name="channel_options">
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92 <param name="extract" type="select" label="Extract channel" >
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93 <option selected="True" value="False">All channels</option>
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94 <option value="True">Extract channel</option>
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95 </param>
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96 <when value="False"> </when>
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97 <when value="True">
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98 <param name="channel" type="integer" value="0" label="Channel id" />
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99 </when>
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100 </conditional>
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101 <conditional name="z_options">
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102 <param label="Extract z-slice" name="extract" type="select">
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103 <option selected="True" value="False">All z-slices</option>
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104 <option value="True">Extract z-slice</option>
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105 </param>
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106 <when value="False"> </when>
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107 <when value="True">
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108 <param name="z" type="integer" value="0" label="Z-slice id" />
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109 </when>
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110 </conditional>
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111 <conditional name="range_options">
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112 <param label="Extract range" name="extract" type="select">
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113 <option selected="True" value="False">All images</option>
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114 <option value="True">Extract range by indicess (inclusive)</option>
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115 </param>
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116 <when value="False"> </when>
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117 <when value="True">
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118 <param name="range_lower" type="integer" value="0" label="Lower image id" />
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119 <param name="range_upper" type="integer" value="1" label="Upper image id" />
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120 </when>
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121 </conditional>
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122 <conditional name="crop_options">
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123 <param label="Extract crop" name="extract" type="select">
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124 <option selected="True" value="False">Full image</option>
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125 <option value="True">Extract crop</option>
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126 </param>
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127 <when value="False"> </when>
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128 <when value="True">
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129 <param name="crop_x" type="integer" value="0" label="X" />
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130 <param name="crop_y" type="integer" value="0" label="Y" />
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131 <param name="crop_width" type="integer" value="512" label="Width" />
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132 <param name="crop_height" type="integer" value="512" label="height" />
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133 </when>
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134 </conditional>
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135 <conditional name="tile_options">
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136 <param label="Tile image" name="extract" type="select">
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137 <option selected="True" value="False">No tiling</option>
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138 <option value="True">Tile image</option>
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139 </param>
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140 <when value="False"> </when>
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141 <when value="True">
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142 <param name="tile_x" type="integer" value="512 " label="Tile width" />
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143 <param name="tile_y" type="integer" value="512 " label="Tile height" />
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144 </when>
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145 </conditional>
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146 <conditional name="pyramid_options">
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147 <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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148 <option selected="True" value="True">Generate Pyramid</option>
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149 <option value="False">No Pyramid</option>
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150 </param>
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151 <when value="True">
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152 <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/>
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153 <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" />
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154 </when>
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155 <when value="False" />
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156 </conditional>
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157 <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/>
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158 <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/>
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159 <param label="Compression" name="compression" type="select">
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160 <option selected="True" value="False">No Compression</option>
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161 <option value="LZW">LZW</option>
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162 <option value="JPEG-2000">JPEG-2000</option>
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163 <option value="JPEG-2000 Lossy">JPEG-2000 Lossy</option>
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164 <option value="JPEG">JPEG</option>
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165 <option value="zlib">zlib</option>
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166 </param>
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167 </inputs>
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168 <outputs>
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169 <data format="tiff" name="output" from_work_dir="result_image">
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170 <change_format>
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171 <when input="out_format" value="tiff" format="tiff" />
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172 <when input="out_format" value="png" format="png" />
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173 <when input="out_format" value="jpg" format="jpg" />
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174 <when input="out_format" value="ome.tiff" format="ome.tiff" />
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175 <when input="out_format" value="jp2" format="jpg" />
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176 <when input="out_format" value="eps" format="eps" />
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177 <when input="out_format" value="avi" format="avi" />
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178 </change_format>
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179 </data>
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180 </outputs>
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181 <tests>
0
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182 <test>
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183 <param name="input_file" value="input.png" />
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184 <param name="out_format" value="tiff" />
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185 <expand macro="tests/intensity_image_diff" name="output" value="res.tiff" ftype="tiff"/>
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186 </test>
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187 <test>
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188 <param name="input_file" value="input.png" />
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189 <param name="out_format" value="ome.tiff" />
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190 <conditional name="pyramid_options">
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191 <param name="generate" value="True"/>
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192 <param name="pyramid_resolutions" value="4"/>
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193 <param name="pyramid_scale" value="2"/>
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194 </conditional>
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195 <expand macro="tests/intensity_image_diff" name="output" value="res.ome.tiff" ftype="ome.tiff"/>
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196 </test>
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197 <test>
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198 <param name="input_file" value="input.tiff" />
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199 <param name="out_format" value="png" />
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200 <expand macro="tests/intensity_image_diff" name="output" value="input.tiff.png" ftype="png"/>
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201 </test>
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202 </tests>
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203 <help>
0
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204
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205 **Converts image format.**
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206
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207 Universial image converter using bioformats.
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208
0
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209 </help>
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210 <citations>
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211 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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212 </citations>
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213 </tool>
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214