Mercurial > repos > imgteam > bfconvert
changeset 0:0bcd0e75812a draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/bfconvert/ commit ebb7b59e3271b15bc67b47f39dcc42bd9ae9a889
| author | imgteam |
|---|---|
| date | Mon, 22 Jul 2019 11:08:32 -0400 |
| parents | |
| children | ba1fe7645bd0 |
| files | bfconvert.xml test-data/input.png test-data/res.tiff |
| diffstat | 3 files changed, 117 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bfconvert.xml Mon Jul 22 11:08:32 2019 -0400 @@ -0,0 +1,117 @@ +<tool id="ip_convertimage" name="Convert image" version="0.1"> + <description>Convert image</description> + <requirements> + <requirement type="package" version="5.7.1">bftools</requirement> + </requirements> + <command> + <![CDATA[ + bfconvert + #if $series_options['extract'] == 'True' + -series $series + #end if + #if $timepoint_options['extract'] == 'True' + -timepoint $timepoint + #end if + #if $channel_options['extract'] == 'True' + -channel $channel + #end if + #if $z_options['extract'] == 'True' + -z $z + #end if + #if $range_options['extract'] == 'True' + -range $range_lower $range_upper + #end if + #if $crop_options['extract'] == 'True' + -crop $crop_x $crop_y $crop_width $crop_height + #end if + '$input_file' ./res.tiff + ]]> + </command> + <inputs> + <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"/> + + <conditional name="series_options"> + <param label="Extract series" name="extract" type="select"> + <option selected="True" value="False">All series</option> + <option value="True">Extract series</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="series" type="integer" value="0" label="Series id" /> + </when> + </conditional> + <conditional name="timepoint_options"> + <param label="Extract timepoint" name="extract" type="select"> + <option selected="True" value="False">All timepoints</option> + <option value="True">Extract timepoint</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="timepoint" type="integer" value="0" label="Timepoint id" /> + </when> + </conditional> + <conditional name="channel_options"> + <param label="Extract channel" name="extract" type="select"> + <option selected="True" value="False">All channels</option> + <option value="True">Extract channel</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="channel" type="integer" value="0" label="Channel id" /> + </when> + </conditional> + <conditional name="z_options"> + <param label="Extract z-slice" name="extract" type="select"> + <option selected="True" value="False">All z-slices</option> + <option value="True">Extract z-slice</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="z" type="integer" value="0" label="Z-slice id" /> + </when> + </conditional> + <conditional name="range_options"> + <param label="Extract range" name="extract" type="select"> + <option selected="True" value="False">All images</option> + <option value="True">Extract range by indicess (inclusive)</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="range_lower" type="integer" value="0" label="Lower image id" /> + <param name="range_upper" type="integer" value="1" label="Upper image id" /> + </when> + </conditional> + <conditional name="crop_options"> + <param label="Extract crop" name="extract" type="select"> + <option selected="True" value="False">Full image</option> + <option value="True">Extract crop</option> + </param> + <when value="False"> </when> + <when value="True"> + <param name="crop_x" type="integer" value="0" label="X" /> + <param name="crop_y" type="integer" value="0" label="Y" /> + <param name="crop_width" type="integer" value="512" label="Width" /> + <param name="crop_height" type="integer" value="512" label="height" /> + </when> + </conditional> + + </inputs> + <outputs> + <data format="tiff" name="output" from_work_dir="res.tiff"/> + </outputs> + <tests> + <test> + <param name="input_file" value="input.png" /> + <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/> + </test> + </tests> + <help> + **What it does** + + Convert image to tiff using bioformats. + </help> + <citations> + <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> + </citations> +</tool> +