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comparison 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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0:bbb307f731c3 1:6317c4a379b2
1 <tool id="ip_convertimage" name="Convert image" version="0.1"> 1 <tool id="ip_convertimage" name="Convert image" version="0.3">
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="5.7.1">bftools</requirement>
5 </requirements> 5 </requirements>
6 <command> 6 <command>
22 -range $range_lower $range_upper 22 -range $range_lower $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_x $crop_y $crop_width $crop_height
26 #end if 26 #end if
27 '$input_file' ./res.tiff 27 #if $tile_options['extract'] == 'True'
28 -tilex $tile_x -tiley $tile_y
29 #end if
30 '$input_file' ./res.$out_format
28 ]]> 31 ]]>
29 </command> 32 </command>
30 <inputs> 33 <inputs>
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"/> 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"/>
35 <param name="out_format" type="select" label="Output data type">
36 <option value="tiff" selected="True">TIFF</option>
37 <option value="png">PNG</option>
38 <option value="jpg">JPEG</option>
39 <option value="ome.tiff">OME TIFF</option>
40 <option value="jp2">JPEG 2000</option>
41 <option value="eps">EPS</option>
42 <option value="avi">AVI</option>
43 </param>
32 44
33 <conditional name="series_options"> 45 <conditional name="series_options">
34 <param label="Extract series" name="extract" type="select"> 46 <param label="Extract series" name="extract" type="select">
35 <option selected="True" value="False">All series</option> 47 <option selected="True" value="False">All series</option>
36 <option value="True">Extract series</option> 48 <option value="True">Extract series</option>
92 <param name="crop_y" type="integer" value="0" label="Y" /> 104 <param name="crop_y" type="integer" value="0" label="Y" />
93 <param name="crop_width" type="integer" value="512" label="Width" /> 105 <param name="crop_width" type="integer" value="512" label="Width" />
94 <param name="crop_height" type="integer" value="512" label="height" /> 106 <param name="crop_height" type="integer" value="512" label="height" />
95 </when> 107 </when>
96 </conditional> 108 </conditional>
97 109 <conditional name="tile_options">
110 <param label="Tile image" name="extract" type="select">
111 <option selected="True" value="False">No tiling</option>
112 <option value="True">Tile image</option>
113 </param>
114 <when value="False"> </when>
115 <when value="True">
116 <param name="tile_x" type="integer" value="512 " label="Tile width" />
117 <param name="tile_y" type="integer" value="512 " label="Tile height" />
118 </when>
119 </conditional>
98 </inputs> 120 </inputs>
99 <outputs> 121 <outputs>
100 <data format="tiff" name="output" from_work_dir="res.tiff"/> 122 <data format="tiff" name="output" from_work_dir="res.tiff">
123 <change_format>
124 <when input="out_format" value="tiff" format="tiff" />
125 <when input="out_format" value="png" format="png" />
126 <when input="out_format" value="jpg" format="jpg" />
127 <when input="out_format" value="ome.tiff" format="tiff" />
128 <when input="out_format" value="jp2" format="jpg" />
129 <when input="out_format" value="eps" format="eps" />
130 <when input="out_format" value="avi" format="avi" />
131 </change_format>
132 </data>
101 </outputs> 133 </outputs>
102 <tests> 134 <tests>
103 <test> 135 <test>
104 <param name="input_file" value="input.png" /> 136 <param name="input_file" value="input.png" />
137 <param name="out_format" value="tiff" />
105 <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/> 138 <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/>
106 </test> 139 </test>
107 </tests> 140 </tests>
108 <help> 141 <help>
109 **What it does** 142 **What it does**