change extra_files_path to files_path

tools/bioformats2raw/bf2raw.xml

@@ -2,7 +2,7 @@
     <description>with Bioformats</description>
     <macros>
          <token name="@TOOL_VERSION@">0.7.0</token>
-         <token name="@VERSION_SUFFIX@">0</token>
+         <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <edam_operations>
         <edam_operation>operation_3443</edam_operation>
@@ -12,19 +12,19 @@
     </requirements>
     <command><![CDATA[
 
-if [ ! -d $output.extra_files_path ];then
-    mkdir -p $output.extra_files_path;
+if [ ! -d $output.files_path ];then
+    mkdir -p $output.files_path;
 fi;
 
 #if str($io_options.input.ext)=='html':
-    #set dirlist=os.listdir($io_options.input.extra_files_path)
+    #set dirlist=os.listdir($io_options.input.files_path)
     #assert len($dirlist) > 0
-    #set input_path=os.path.join(str($io_options.input.extra_files_path), str($dirlist[0]))
+    #set input_path=os.path.join(str($io_options.input.files_path), str($dirlist[0]))
 #else:
     #set input_path=$io_options.input
 #end if
 
-bioformats2raw $input_path $output.extra_files_path/$io_options.output_name
+bioformats2raw $input_path $output.files_path/$io_options.output_name
 #if $bf2raw_params.multiscales['options'] == 'auto':
     --target-min-size $bf2raw_params.multiscales.min_xy_size
 #elif $bf2raw_params.multiscales['options'] == 'manual':
@@ -47,9 +47,9 @@ $bf2raw_params.droptop
 
     ]]></command>
     <inputs>
-        <section name="io_options" title="Input-output paths">
+        <section name="io_options" title="Input-output paths" expanded="true">
             <param name="input" 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" label="Input image located in Galaxy history"/>
-            <param name="output_name" type="text" value="data.zarr" label="Output zarr data"/>
+            <param name="output_name" type="text" value="output.ome.zarr" label="Output zarr data"/>
         </section>
         <section name="bf2raw_params" title="Parameters fed to file conversion module">
             <conditional name="multiscales" >
@@ -106,17 +106,17 @@ $bf2raw_params.droptop
             </output>
         </test>
         <test expect_num_outputs="1">
-            <param name="input" value="astronaut.png"/>
-            <param name="output_name" value="astronaut.ome.zarr" />
+            <param name="input" value="coins.png"/>
+            <param name="output_name" value="coins.ome.zarr" />
             <output name="output" ftype="html">
-                <extra_files type="file" name="astronaut.ome.zarr/.zgroup" value="astronaut.ome.zarr/.zgroup" />
+                <extra_files type="file" name="coins.ome.zarr/.zgroup" value="coins.ome.zarr/.zgroup" />
             </output>
         </test>
         <test expect_num_outputs="1">
-            <param name="input" value="rocket.jpg"/>
-            <param name="output_name" value="rocket.ome.zarr" />
+            <param name="input" value="camera.jpg"/>
+            <param name="output_name" value="camera.ome.zarr" />
             <output name="output" ftype="html">
-                <extra_files type="file" name="rocket.ome.zarr/.zattrs" value="rocket.ome.zarr/.zattrs" />
+                <extra_files type="file" name="camera.ome.zarr/.zattrs" value="camera.ome.zarr/.zattrs" />
             </output>
         </test>
     </tests>
@@ -130,4 +130,4 @@ Bioformats-based tool that converts a wide range of image file formats to the cl
     <citations>
         <citation type="doi">https://doi.org/10.5281/zenodo.5548102 </citation>
     </citations>
-</tool>
+</tool>

tools/bioformats2raw/test-data/rocket.ome.zarr/0/.zattrs → tools/bioformats2raw/test-data/camera.ome.zarr/0/.zattrs

@@ -20,7 +20,7 @@
       "name" : "x",
       "type" : "space"
     } ],
-    "name" : "rocket.jpg",
+    "name" : "camera.jpg",
     "datasets" : [ {
       "path" : "0",
       "coordinateTransformations" : [ {
@@ -44,7 +44,7 @@
   } ],
   "omero" : {
     "channels" : [ {
-      "color" : "FF0000",
+      "color" : "808080",
       "coefficient" : 1,
       "active" : true,
       "label" : "Channel 0",
@@ -56,36 +56,10 @@
       },
       "family" : "linear",
       "inverted" : false
-    }, {
-      "color" : "00FF00",
-      "coefficient" : 1,
-      "active" : true,
-      "label" : "Channel 1",
-      "window" : {
-        "min" : 0.0,
-        "max" : 255.0,
-        "start" : 0.0,
-        "end" : 255.0
-      },
-      "family" : "linear",
-      "inverted" : false
-    }, {
-      "color" : "0000FF",
-      "coefficient" : 1,
-      "active" : true,
-      "label" : "Channel 2",
-      "window" : {
-        "min" : 0.0,
-        "max" : 255.0,
-        "start" : 0.0,
-        "end" : 255.0
-      },
-      "family" : "linear",
-      "inverted" : false
     } ],
     "rdefs" : {
       "defaultT" : 0,
-      "model" : "color",
+      "model" : "greyscale",
       "defaultZ" : 0
     }
   }

tools/bioformats2raw/test-data/astronaut.ome.zarr/0/1/.zarray → tools/bioformats2raw/test-data/camera.ome.zarr/0/0/.zarray

@@ -1,5 +1,5 @@
 {
-  "chunks" : [ 1, 1, 1, 240, 320 ],
+  "chunks" : [ 1, 1, 1, 96, 96 ],
   "compressor" : {
     "clevel" : 5,
     "blocksize" : 0,
@@ -11,7 +11,7 @@
   "fill_value" : 0,
   "filters" : null,
   "order" : "C",
-  "shape" : [ 1, 3, 1, 240, 320 ],
+  "shape" : [ 1, 1, 1, 480, 640 ],
   "dimension_separator" : "/",
   "zarr_format" : 2
 }

tools/bioformats2raw/test-data/astronaut.ome.zarr/0/0/.zarray → tools/bioformats2raw/test-data/camera.ome.zarr/0/1/.zarray

@@ -1,5 +1,5 @@
 {
-  "chunks" : [ 1, 1, 1, 480, 640 ],
+  "chunks" : [ 1, 1, 1, 96, 96 ],
   "compressor" : {
     "clevel" : 5,
     "blocksize" : 0,
@@ -11,7 +11,7 @@
   "fill_value" : 0,
   "filters" : null,
   "order" : "C",
-  "shape" : [ 1, 3, 1, 480, 640 ],
+  "shape" : [ 1, 1, 1, 240, 320 ],
   "dimension_separator" : "/",
   "zarr_format" : 2
 }

tools/bioformats2raw/test-data/astronaut.ome.zarr/0/2/.zarray → tools/bioformats2raw/test-data/camera.ome.zarr/0/2/.zarray

@@ -1,5 +1,5 @@
 {
-  "chunks" : [ 1, 1, 1, 120, 160 ],
+  "chunks" : [ 1, 1, 1, 96, 96 ],
   "compressor" : {
     "clevel" : 5,
     "blocksize" : 0,
@@ -11,7 +11,7 @@
   "fill_value" : 0,
   "filters" : null,
   "order" : "C",
-  "shape" : [ 1, 3, 1, 120, 160 ],
+  "shape" : [ 1, 1, 1, 120, 160 ],
   "dimension_separator" : "/",
   "zarr_format" : 2
 }

tools/bioformats2raw/test-data/camera.ome.zarr/OME/METADATA.ome.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="camera.jpg"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="1" SizeT="1" SizeX="640" SizeY="480" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/></Pixels></Image></OME>

tools/bioformats2raw/test-data/astronaut.ome.zarr/0/.zattrs → tools/bioformats2raw/test-data/coins.ome.zarr/0/.zattrs

@@ -20,7 +20,7 @@
       "name" : "x",
       "type" : "space"
     } ],
-    "name" : "astronaut.png",
+    "name" : "coins.png",
     "datasets" : [ {
       "path" : "0",
       "coordinateTransformations" : [ {
@@ -44,7 +44,7 @@
   } ],
   "omero" : {
     "channels" : [ {
-      "color" : "FF0000",
+      "color" : "808080",
       "coefficient" : 1,
       "active" : true,
       "label" : "Channel 0",
@@ -56,36 +56,10 @@
       },
       "family" : "linear",
       "inverted" : false
-    }, {
-      "color" : "00FF00",
-      "coefficient" : 1,
-      "active" : true,
-      "label" : "Channel 1",
-      "window" : {
-        "min" : 0.0,
-        "max" : 255.0,
-        "start" : 0.0,
-        "end" : 255.0
-      },
-      "family" : "linear",
-      "inverted" : false
-    }, {
-      "color" : "0000FF",
-      "coefficient" : 1,
-      "active" : true,
-      "label" : "Channel 2",
-      "window" : {
-        "min" : 0.0,
-        "max" : 255.0,
-        "start" : 0.0,
-        "end" : 255.0
-      },
-      "family" : "linear",
-      "inverted" : false
     } ],
     "rdefs" : {
       "defaultT" : 0,
-      "model" : "color",
+      "model" : "greyscale",
       "defaultZ" : 0
     }
   }

tools/bioformats2raw/test-data/rocket.ome.zarr/0/0/.zarray → tools/bioformats2raw/test-data/coins.ome.zarr/0/0/.zarray

@@ -1,5 +1,5 @@
 {
-  "chunks" : [ 1, 1, 1, 427, 640 ],
+  "chunks" : [ 1, 1, 1, 96, 96 ],
   "compressor" : {
     "clevel" : 5,
     "blocksize" : 0,
@@ -11,7 +11,7 @@
   "fill_value" : 0,
   "filters" : null,
   "order" : "C",
-  "shape" : [ 1, 3, 1, 427, 640 ],
+  "shape" : [ 1, 1, 1, 480, 640 ],
   "dimension_separator" : "/",
   "zarr_format" : 2
 }

tools/bioformats2raw/test-data/coins.ome.zarr/0/1/.zarray

@@ -0,0 +1,17 @@
+{
+  "chunks" : [ 1, 1, 1, 96, 96 ],
+  "compressor" : {
+    "clevel" : 5,
+    "blocksize" : 0,
+    "shuffle" : 1,
+    "cname" : "lz4",
+    "id" : "blosc"
+  },
+  "dtype" : "|u1",
+  "fill_value" : 0,
+  "filters" : null,
+  "order" : "C",
+  "shape" : [ 1, 1, 1, 240, 320 ],
+  "dimension_separator" : "/",
+  "zarr_format" : 2
+}

tools/bioformats2raw/test-data/coins.ome.zarr/0/2/.zarray

@@ -0,0 +1,17 @@
+{
+  "chunks" : [ 1, 1, 1, 96, 96 ],
+  "compressor" : {
+    "clevel" : 5,
+    "blocksize" : 0,
+    "shuffle" : 1,
+    "cname" : "lz4",
+    "id" : "blosc"
+  },
+  "dtype" : "|u1",
+  "fill_value" : 0,
+  "filters" : null,
+  "order" : "C",
+  "shape" : [ 1, 1, 1, 120, 160 ],
+  "dimension_separator" : "/",
+  "zarr_format" : 2
+}

tools/bioformats2raw/test-data/coins.ome.zarr/OME/METADATA.ome.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd"><Image ID="Image:0" Name="coins.png"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="1" SizeT="1" SizeX="640" SizeY="480" SizeZ="1" Type="uint8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><MetadataOnly/></Pixels></Image></OME>

tools/bioformats2raw/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/0/.zarray

@@ -1,5 +1,5 @@
 {
-  "chunks" : [ 1, 1, 1, 263, 263 ],
+  "chunks" : [ 1, 1, 1, 96, 96 ],
   "compressor" : {
     "clevel" : 5,
     "blocksize" : 0,

tools/bioformats2raw/test-data/xyz_8bit__mitotic_plate_calibrated.ome.zarr/0/1/.zarray

@@ -1,5 +1,5 @@
 {
-  "chunks" : [ 1, 1, 1, 131, 131 ],
+  "chunks" : [ 1, 1, 1, 96, 96 ],
   "compressor" : {
     "clevel" : 5,
     "blocksize" : 0,