| Previous changeset 5:85edbb7a436b (2023-11-10) |
|
Commit message:
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/bfconvert/ commit c045f067a57e8308308cf6329060c7ccd3fc372f |
|
modified:
bfconvert.xml test-data/res.ome.tiff test-data/res.tiff |
|
added:
creators.xml tests.xml |
| b |
| diff -r 85edbb7a436b -r fcadded98e61 bfconvert.xml --- a/bfconvert.xml Fri Nov 10 14:23:17 2023 +0000 +++ b/bfconvert.xml Thu Apr 04 15:23:54 2024 +0000 |
| [ |
| b'@@ -1,15 +1,25 @@\n-<tool id="ip_convertimage" name="Convert image format" version="6.7.0+galaxy2">\n- <description>with Bioformats</description>\n- <edam_operations>\n- <edam_operation>operation_3443</edam_operation>\n- </edam_operations>\n- <xrefs>\n- <xref type="biii">python-bioformats</xref>\n- </xrefs>\n- <requirements>\n- <requirement type="package" version="6.7.0">bftools</requirement>\n- </requirements>\n- <command> \n+<tool id="ip_convertimage" name="Convert image format" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">\n+ <description>with Bioformats</description>\n+ <macros>\n+ <import>creators.xml</import>\n+ <import>tests.xml</import>\n+ <token name="@TOOL_VERSION@">6.7.0</token>\n+ <token name="@VERSION_SUFFIX@">3</token>\n+ </macros>\n+ <creator>\n+ <expand macro="creators/alliecreason"/>\n+ <expand macro="creators/bmcv"/>\n+ </creator>\n+ <edam_operations>\n+ <edam_operation>operation_3443</edam_operation>\n+ </edam_operations>\n+ <xrefs>\n+ <xref type="biii">python-bioformats</xref>\n+ </xrefs>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">bftools</requirement>\n+ </requirements>\n+ <command> \n <![CDATA[ \n bfconvert \n #if $series_options[\'extract\'] == \'True\'\n@@ -45,134 +55,134 @@\n \'$input_file\' \'./res.$out_format\' &&\n mv \'./res.$out_format\' ./result_image\n ]]>\n- </command>\n- <inputs>\n- <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"/>\n- <param name="out_format" type="select" label="Output data type">\n- <option value="tiff" selected="True">TIFF</option>\n- <option value="png">PNG</option>\n- <option value="jpg">JPEG</option>\n- <option value="ome.tiff">OME TIFF</option>\n- <option value="jp2">JPEG 2000</option>\n- <option value="eps">EPS</option>\n- <option value="avi">AVI</option>\n- </param>\n-\n- <conditional name="series_options">\n- <param label="Extract series" name="extract" type="select">\n- <option selected="True" value="False">All series</option>\n- <option value="True">Extract series</option>\n- </param>\n- <when value="False"> </when>\n- <when value="True">\n- <param name="series" type="integer" value="0" label="Series id" />\n- </when>\n- </conditional>\n- <conditional name="timepoint_options">\n- <param name="extract" type="select" label="Extract timepoint">\n- <option selected="True" value="False">All timepoints</option>\n- <option value="True">Extract timepoint</option>\n- </param>\n- <when value="False"></when>\n- <when value="True">\n- <param name="timepoint" type="integer" value="0" label="Timepoint ID" />\n- </when>\n- </conditional>\n- <conditional name="channel_options">\n- <param name="extract" type="select" label="Extract channel" >\n- <option selected="True" value="False">All channels</option>\n- <option value='..b'\n+ <when value="False"> </when>\n+ <when value="True">\n+ <param name="tile_x" type="integer" value="512 " label="Tile width" />\n+ <param name="tile_y" type="integer" value="512 " label="Tile height" />\n+ </when>\n+ </conditional>\n+ <conditional name="pyramid_options">\n+ <param label="Pyramid image" name="generate" type="select" help="Pyramids will be generated only if the selected output format supports pyramids (OME TIFF, JPEG 2000)."><!-- see: https://docs.openmicroscopy.org/bio-formats/6.7.0/supported-formats.html -->\n+ <option selected="True" value="True">Generate Pyramid</option>\n+ <option value="False">No Pyramid</option>\n+ </param>\n+ <when value="True">\n+ <param name="pyramid_resolutions" type="integer" value="4" label="Pyramid Resolutions"/>\n+ <param name="pyramid_scale" type="integer" value="2" label="Pyramid Scale" />\n+ </when>\n+ <when value="False" />\n+ </conditional>\n+ <param name="bigtiff" label="Big TIFF" type="boolean" checked="false" truevalue="-bigtiff" falsevalue=""/>\n+ <param name="noflat" label="No Flatten" type="boolean" checked="true" truevalue="-noflat" falsevalue=""/>\n+ <param label="Compression" name="compression" type="select">\n+ <option selected="True" value="False">No Compression</option>\n+ <option value="LZW">LZW</option>\n+ <option value="JPEG-2000">JPEG-2000</option>\n+ <option value="JPEG-2000 Lossy">JPEG-2000 Lossy</option>\n+ <option value="JPEG">JPEG</option>\n+ <option value="zlib">zlib</option>\n+ </param> \n+ </inputs>\n+ <outputs>\n+ <data format="tiff" name="output" from_work_dir="result_image">\n+ <change_format>\n+ <when input="out_format" value="tiff" format="tiff" />\n+ <when input="out_format" value="png" format="png" />\n+ <when input="out_format" value="jpg" format="jpg" />\n+ <when input="out_format" value="ome.tiff" format="ome.tiff" />\n+ <when input="out_format" value="jp2" format="jpg" />\n+ <when input="out_format" value="eps" format="eps" />\n+ <when input="out_format" value="avi" format="avi" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n <test>\n <param name="input_file" value="input.png" />\n- <param name="out_format" value="tiff" /> \n- <output name="output" value="res.tiff" ftype="tiff" compare="sim_size"/>\n+ <param name="out_format" value="tiff" />\n+ <expand macro="tests/intensity_image_diff" name="output" value="res.tiff" ftype="tiff"/>\n </test>\n <test>\n <param name="input_file" value="input.png" />\n@@ -182,18 +192,20 @@\n <param name="pyramid_resolutions" value="4"/>\n <param name="pyramid_scale" value="2"/>\n </conditional>\n- <output name="output" value="res.ome.tiff" ftype="ome.tiff" compare="sim_size"/>\n+ <expand macro="tests/intensity_image_diff" name="output" value="res.ome.tiff" ftype="ome.tiff"/>\n </test>\n <test>\n <param name="input_file" value="input.tiff" />\n <param name="out_format" value="png" />\n- <output name="output" value="input.tiff.png" ftype="png" compare="sim_size"/>\n+ <expand macro="tests/intensity_image_diff" name="output" value="input.tiff.png" ftype="png"/>\n </test>\n- </tests> \n- <help>\n- **What it does**\n+ </tests> \n+ <help>\n \n- Universial image converter using bioformats.\n+ **Converts image format.**\n+\n+ Universial image converter using bioformats.\n+\n </help>\n <citations>\n <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>\n' |
| b |
| diff -r 85edbb7a436b -r fcadded98e61 creators.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Thu Apr 04 15:23:54 2024 +0000 |
| b |
| @@ -0,0 +1,23 @@ +<macros> + + <xml name="creators/bmcv"> + <organization name="Biomedical Computer Vision Group, Heidelberg Universtiy" alternateName="BMCV" url="http://www.bioquant.uni-heidelberg.de/research/groups/biomedical_computer_vision.html" /> + <yield /> + </xml> + + <xml name="creators/alliecreason"> + <person givenName="Allison" familyName="Creason"/> + <yield/> + </xml> + + <xml name="creators/bugraoezdemir"> + <person givenName="Bugra" familyName="Oezdemir"/> + <yield/> + </xml> + + <xml name="creators/thawn"> + <person givenName="Till" familyName="Korten"/> + <yield/> + </xml> + +</macros> |
| b |
| diff -r 85edbb7a436b -r fcadded98e61 test-data/res.ome.tiff |
| b |
| Binary file test-data/res.ome.tiff has changed |
| b |
| diff -r 85edbb7a436b -r fcadded98e61 test-data/res.tiff |
| b |
| Binary file test-data/res.tiff has changed |
| b |
| diff -r 85edbb7a436b -r fcadded98e61 tests.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Thu Apr 04 15:23:54 2024 +0000 |
| b |
| @@ -0,0 +1,95 @@ +<macros> + + <!-- Macros for verification of image outputs --> + + <xml + name="tests/binary_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/label_image_diff" + tokens="name,value,ftype,metric,eps,pin_labels" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <xml + name="tests/intensity_image_diff" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <output name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </output> + + </xml> + + <!-- Variants of the above for verification of collection elements --> + + <xml + name="tests/binary_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="mae" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="0"> + <assert_contents> + <has_image_n_labels n="2"/> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/label_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="iou" + token_eps="0.01" + token_pin_labels="0"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@" pin_labels="@PIN_LABELS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + + <xml + name="tests/intensity_image_diff/element" + tokens="name,value,ftype,metric,eps" + token_metric="rms" + token_eps="0.01"> + + <element name="@NAME@" value="@VALUE@" ftype="@FTYPE@" compare="image_diff" metric="@METRIC@" eps="@EPS@"> + <assert_contents> + <yield/> + </assert_contents> + </element> + + </xml> + +</macros> |