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annotate bfconvert.xml @ 0:bbb307f731c3 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
author imgteam
date Mon, 22 Jul 2019 11:09:08 -0400
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children 6317c4a379b2
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0
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
imgteam
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1 <tool id="ip_convertimage" name="Convert image" version="0.1">
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>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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4 <requirement type="package" version="5.7.1">bftools</requirement>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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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>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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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
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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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 $crop_height
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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26 #end if
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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27 '$input_file' ./res.tiff
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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28 ]]>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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29 </command>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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30 <inputs>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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31 <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"/>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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32
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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33 <conditional name="series_options">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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34 <param label="Extract series" name="extract" type="select">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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35 <option selected="True" value="False">All series</option>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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36 <option value="True">Extract series</option>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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37 </param>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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38 <when value="False"> </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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39 <when value="True">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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40 <param name="series" type="integer" value="0" label="Series id" />
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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41 </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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42 </conditional>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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43 <conditional name="timepoint_options">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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44 <param label="Extract timepoint" name="extract" type="select">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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45 <option selected="True" value="False">All timepoints</option>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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46 <option value="True">Extract timepoint</option>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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47 </param>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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48 <when value="False"> </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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49 <when value="True">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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50 <param name="timepoint" type="integer" value="0" label="Timepoint id" />
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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51 </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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52 </conditional>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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53 <conditional name="channel_options">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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54 <param label="Extract channel" name="extract" type="select">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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55 <option selected="True" value="False">All channels</option>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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56 <option value="True">Extract channel</option>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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57 </param>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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58 <when value="False"> </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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59 <when value="True">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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60 <param name="channel" type="integer" value="0" label="Channel id" />
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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61 </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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62 </conditional>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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63 <conditional name="z_options">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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64 <param label="Extract z-slice" name="extract" type="select">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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65 <option selected="True" value="False">All z-slices</option>
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66 <option value="True">Extract z-slice</option>
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67 </param>
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68 <when value="False"> </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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69 <when value="True">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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70 <param name="z" type="integer" value="0" label="Z-slice id" />
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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71 </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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72 </conditional>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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73 <conditional name="range_options">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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74 <param label="Extract range" name="extract" type="select">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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75 <option selected="True" value="False">All images</option>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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76 <option value="True">Extract range by indicess (inclusive)</option>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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77 </param>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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78 <when value="False"> </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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79 <when value="True">
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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80 <param name="range_lower" type="integer" value="0" label="Lower image id" />
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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81 <param name="range_upper" type="integer" value="1" label="Upper image id" />
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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82 </when>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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83 </conditional>
bbb307f731c3 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
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84 <conditional name="crop_options">
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85 <param label="Extract crop" name="extract" type="select">
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86 <option selected="True" value="False">Full image</option>
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87 <option value="True">Extract crop</option>
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88 </param>
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89 <when value="False"> </when>
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90 <when value="True">
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91 <param name="crop_x" type="integer" value="0" label="X" />
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92 <param name="crop_y" type="integer" value="0" label="Y" />
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93 <param name="crop_width" type="integer" value="512" label="Width" />
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94 <param name="crop_height" type="integer" value="512" label="height" />
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95 </when>
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96 </conditional>
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97
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98 </inputs>
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99 <outputs>
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100 <data format="tiff" name="output" from_work_dir="res.tiff"/>
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101 </outputs>
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102 <tests>
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103 <test>
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104 <param name="input_file" value="input.png" />
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105 <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/>
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106 </test>
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107 </tests>
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108 <help>
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109 **What it does**
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110
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111 Convert image to tiff using bioformats.
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112 </help>
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113 <citations>
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114 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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115 </citations>
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116 </tool>
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117