Mercurial > repos > imgteam > bfconvert
comparison bfconvert.xml @ 0:bbb307f731c3 draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
author | imgteam |
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date | Mon, 22 Jul 2019 11:09:08 -0400 (2019-07-22) |
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children | 6317c4a379b2 |
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-1:000000000000 | 0:bbb307f731c3 |
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1 <tool id="ip_convertimage" name="Convert image" version="0.1"> | |
2 <description>Convert image</description> | |
3 <requirements> | |
4 <requirement type="package" version="5.7.1">bftools</requirement> | |
5 </requirements> | |
6 <command> | |
7 <![CDATA[ | |
8 bfconvert | |
9 #if $series_options['extract'] == 'True' | |
10 -series $series | |
11 #end if | |
12 #if $timepoint_options['extract'] == 'True' | |
13 -timepoint $timepoint | |
14 #end if | |
15 #if $channel_options['extract'] == 'True' | |
16 -channel $channel | |
17 #end if | |
18 #if $z_options['extract'] == 'True' | |
19 -z $z | |
20 #end if | |
21 #if $range_options['extract'] == 'True' | |
22 -range $range_lower $range_upper | |
23 #end if | |
24 #if $crop_options['extract'] == 'True' | |
25 -crop $crop_x $crop_y $crop_width $crop_height | |
26 #end if | |
27 '$input_file' ./res.tiff | |
28 ]]> | |
29 </command> | |
30 <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"/> | |
32 | |
33 <conditional name="series_options"> | |
34 <param label="Extract series" name="extract" type="select"> | |
35 <option selected="True" value="False">All series</option> | |
36 <option value="True">Extract series</option> | |
37 </param> | |
38 <when value="False"> </when> | |
39 <when value="True"> | |
40 <param name="series" type="integer" value="0" label="Series id" /> | |
41 </when> | |
42 </conditional> | |
43 <conditional name="timepoint_options"> | |
44 <param label="Extract timepoint" name="extract" type="select"> | |
45 <option selected="True" value="False">All timepoints</option> | |
46 <option value="True">Extract timepoint</option> | |
47 </param> | |
48 <when value="False"> </when> | |
49 <when value="True"> | |
50 <param name="timepoint" type="integer" value="0" label="Timepoint id" /> | |
51 </when> | |
52 </conditional> | |
53 <conditional name="channel_options"> | |
54 <param label="Extract channel" name="extract" type="select"> | |
55 <option selected="True" value="False">All channels</option> | |
56 <option value="True">Extract channel</option> | |
57 </param> | |
58 <when value="False"> </when> | |
59 <when value="True"> | |
60 <param name="channel" type="integer" value="0" label="Channel id" /> | |
61 </when> | |
62 </conditional> | |
63 <conditional name="z_options"> | |
64 <param label="Extract z-slice" name="extract" type="select"> | |
65 <option selected="True" value="False">All z-slices</option> | |
66 <option value="True">Extract z-slice</option> | |
67 </param> | |
68 <when value="False"> </when> | |
69 <when value="True"> | |
70 <param name="z" type="integer" value="0" label="Z-slice id" /> | |
71 </when> | |
72 </conditional> | |
73 <conditional name="range_options"> | |
74 <param label="Extract range" name="extract" type="select"> | |
75 <option selected="True" value="False">All images</option> | |
76 <option value="True">Extract range by indicess (inclusive)</option> | |
77 </param> | |
78 <when value="False"> </when> | |
79 <when value="True"> | |
80 <param name="range_lower" type="integer" value="0" label="Lower image id" /> | |
81 <param name="range_upper" type="integer" value="1" label="Upper image id" /> | |
82 </when> | |
83 </conditional> | |
84 <conditional name="crop_options"> | |
85 <param label="Extract crop" name="extract" type="select"> | |
86 <option selected="True" value="False">Full image</option> | |
87 <option value="True">Extract crop</option> | |
88 </param> | |
89 <when value="False"> </when> | |
90 <when value="True"> | |
91 <param name="crop_x" type="integer" value="0" label="X" /> | |
92 <param name="crop_y" type="integer" value="0" label="Y" /> | |
93 <param name="crop_width" type="integer" value="512" label="Width" /> | |
94 <param name="crop_height" type="integer" value="512" label="height" /> | |
95 </when> | |
96 </conditional> | |
97 | |
98 </inputs> | |
99 <outputs> | |
100 <data format="tiff" name="output" from_work_dir="res.tiff"/> | |
101 </outputs> | |
102 <tests> | |
103 <test> | |
104 <param name="input_file" value="input.png" /> | |
105 <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/> | |
106 </test> | |
107 </tests> | |
108 <help> | |
109 **What it does** | |
110 | |
111 Convert image to tiff using bioformats. | |
112 </help> | |
113 <citations> | |
114 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> | |
115 </citations> | |
116 </tool> | |
117 |