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annotate bfconvert.xml @ 1:6317c4a379b2 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
author imgteam
date Mon, 22 Jul 2019 12:45:14 -0400
parents bbb307f731c3
children b07f4839ca77
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6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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1 <tool id="ip_convertimage" name="Convert image" version="0.3">
0
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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2 <description>Convert image</description>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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3 <requirements>
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4 <requirement type="package" version="5.7.1">bftools</requirement>
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5 </requirements>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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6 <command>
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7 <![CDATA[
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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8 bfconvert
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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9 #if $series_options['extract'] == 'True'
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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10 -series $series
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11 #end if
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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12 #if $timepoint_options['extract'] == 'True'
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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13 -timepoint $timepoint
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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14 #end if
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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15 #if $channel_options['extract'] == 'True'
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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16 -channel $channel
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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17 #end if
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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18 #if $z_options['extract'] == 'True'
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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19 -z $z
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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20 #end if
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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21 #if $range_options['extract'] == 'True'
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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22 -range $range_lower $range_upper
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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23 #end if
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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24 #if $crop_options['extract'] == 'True'
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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25 -crop $crop_x $crop_y $crop_width $crop_height
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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26 #end if
1
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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27 #if $tile_options['extract'] == 'True'
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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28 -tilex $tile_x -tiley $tile_y
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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29 #end if
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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30 '$input_file' ./res.$out_format
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bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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31 ]]>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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32 </command>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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33 <inputs>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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34 <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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6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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35 <param name="out_format" type="select" label="Output data type">
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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36 <option value="tiff" selected="True">TIFF</option>
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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37 <option value="png">PNG</option>
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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38 <option value="jpg">JPEG</option>
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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39 <option value="ome.tiff">OME TIFF</option>
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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40 <option value="jp2">JPEG 2000</option>
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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41 <option value="eps">EPS</option>
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42 <option value="avi">AVI</option>
6317c4a379b2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit 76b4e79c46db8a40df07e429bc5e9aa8d395d5f6
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43 </param>
0
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44
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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45 <conditional name="series_options">
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46 <param label="Extract series" name="extract" type="select">
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47 <option selected="True" value="False">All series</option>
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48 <option value="True">Extract series</option>
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49 </param>
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50 <when value="False"> </when>
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51 <when value="True">
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52 <param name="series" type="integer" value="0" label="Series id" />
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53 </when>
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54 </conditional>
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55 <conditional name="timepoint_options">
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56 <param label="Extract timepoint" name="extract" type="select">
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57 <option selected="True" value="False">All timepoints</option>
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58 <option value="True">Extract timepoint</option>
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59 </param>
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60 <when value="False"> </when>
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61 <when value="True">
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62 <param name="timepoint" type="integer" value="0" label="Timepoint id" />
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63 </when>
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64 </conditional>
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65 <conditional name="channel_options">
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66 <param label="Extract channel" name="extract" type="select">
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67 <option selected="True" value="False">All channels</option>
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68 <option value="True">Extract channel</option>
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69 </param>
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70 <when value="False"> </when>
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71 <when value="True">
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72 <param name="channel" type="integer" value="0" label="Channel id" />
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73 </when>
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74 </conditional>
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75 <conditional name="z_options">
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76 <param label="Extract z-slice" name="extract" type="select">
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77 <option selected="True" value="False">All z-slices</option>
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78 <option value="True">Extract z-slice</option>
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79 </param>
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80 <when value="False"> </when>
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81 <when value="True">
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82 <param name="z" type="integer" value="0" label="Z-slice id" />
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83 </when>
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84 </conditional>
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85 <conditional name="range_options">
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86 <param label="Extract range" name="extract" type="select">
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87 <option selected="True" value="False">All images</option>
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88 <option value="True">Extract range by indicess (inclusive)</option>
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89 </param>
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90 <when value="False"> </when>
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91 <when value="True">
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92 <param name="range_lower" type="integer" value="0" label="Lower image id" />
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93 <param name="range_upper" type="integer" value="1" label="Upper image id" />
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94 </when>
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95 </conditional>
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96 <conditional name="crop_options">
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97 <param label="Extract crop" name="extract" type="select">
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98 <option selected="True" value="False">Full image</option>
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99 <option value="True">Extract crop</option>
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100 </param>
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101 <when value="False"> </when>
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102 <when value="True">
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103 <param name="crop_x" type="integer" value="0" label="X" />
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104 <param name="crop_y" type="integer" value="0" label="Y" />
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105 <param name="crop_width" type="integer" value="512" label="Width" />
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106 <param name="crop_height" type="integer" value="512" label="height" />
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107 </when>
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108 </conditional>
1
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109 <conditional name="tile_options">
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110 <param label="Tile image" name="extract" type="select">
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111 <option selected="True" value="False">No tiling</option>
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112 <option value="True">Tile image</option>
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113 </param>
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114 <when value="False"> </when>
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115 <when value="True">
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116 <param name="tile_x" type="integer" value="512 " label="Tile width" />
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117 <param name="tile_y" type="integer" value="512 " label="Tile height" />
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118 </when>
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119 </conditional>
0
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120 </inputs>
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121 <outputs>
1
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122 <data format="tiff" name="output" from_work_dir="res.tiff">
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123 <change_format>
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124 <when input="out_format" value="tiff" format="tiff" />
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125 <when input="out_format" value="png" format="png" />
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126 <when input="out_format" value="jpg" format="jpg" />
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127 <when input="out_format" value="ome.tiff" format="tiff" />
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128 <when input="out_format" value="jp2" format="jpg" />
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129 <when input="out_format" value="eps" format="eps" />
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130 <when input="out_format" value="avi" format="avi" />
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131 </change_format>
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132 </data>
0
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133 </outputs>
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134 <tests>
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135 <test>
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136 <param name="input_file" value="input.png" />
1
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137 <param name="out_format" value="tiff" />
0
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138 <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/>
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139 </test>
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140 </tests>
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141 <help>
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142 **What it does**
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143
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144 Convert image to tiff using bioformats.
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145 </help>
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146 <citations>
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147 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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148 </citations>
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149 </tool>
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150