Mercurial > repos > imgteam > bfconvert

comparison bfconvert.xml @ 0:bbb307f731c3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
parents
children 6317c4a379b2
comparison
equal deleted inserted replaced
-1:000000000000 0:bbb307f731c3
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