Mercurial > repos > iuc > imagej2_convert_format

changeset 2:cf9ed4ef641d draft

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planemo upload commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
author iuc
date Fri, 26 Jun 2015 05:28:18 -0400
parents 14d09b0ab9e1
children 9a24b7e68010
files imagej2_base_utils.py imagej2_convert_format.xml imagej2_macros.xml
diffstat 3 files changed, 31 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/imagej2_base_utils.py	Fri Jun 19 16:59:08 2015 -0400
+++ b/imagej2_base_utils.py	Fri Jun 26 05:28:18 2015 -0400
@@ -95,7 +95,7 @@
     if max_heap_size_type == 'default':
         return None
     if max_heap_size_type == 'megabytes':
-        if max_heap_size % 1024 not in [ 0, 256, 512 ]:
+        if int( max_heap_size ) % 1024 not in [ 0, 256, 512 ]:
             return None
         return '%sm' % str( max_heap_size )
     if max_heap_size_type == 'gigabytes':
--- a/imagej2_convert_format.xml	Fri Jun 19 16:59:08 2015 -0400
+++ b/imagej2_convert_format.xml	Fri Jun 26 05:28:18 2015 -0400
@@ -10,8 +10,7 @@
         imagej2_convert_format.py
         --in_fname "$input"
         --input_datatype $input.ext
-        --max_heap_size_type $set_max_heap_size.max_heap_size_type
-        --max_heap_size $set_max_heap_size.max_heap_size
+        @max_heap_size_args@
         --output_datatype $output_datatype
         --out_fname "$output"
 ]]>
@@ -65,5 +64,5 @@
 ]]>
 
     </help>
-    <expand macro="citations" />
+    <expand macro="bioformats_fiji_javabridge_citations" />
 </tool>
--- a/imagej2_macros.xml	Fri Jun 19 16:59:08 2015 -0400
+++ b/imagej2_macros.xml	Fri Jun 26 05:28:18 2015 -0400
@@ -59,6 +59,10 @@
             </when>
         </conditional>
     </xml>
+    <token name="@max_heap_size_args@">
+        --max_heap_size_type $set_max_heap_size.max_heap_size_type
+        --max_heap_size $set_max_heap_size.max_heap_size
+    </token>
     <xml name="image_datatypes">
         <option value="bmp">bmp</option>
         <option value="gif">gif</option>
@@ -66,12 +70,35 @@
         <option value="png" selected="true">png</option>
         <option value="tiff">tiff</option>
     </xml>
+    <xml name="bunwarpj_citations">
+        <citations>
+            <citation type="bibtex">
+                @InProceedings(Arganda-Carreras2006,
+                    author =     "Ignacio Arganda-Carreras and
+                                        Carlos Oscar S{\'a}nchez Sorzano and
+                                        Roberto Marabini and
+                                        Jos{\'e} Mar\'{\i}a Carazo and
+                                        Carlos Ortiz-de-Solorzano and
+                                        Jan Kybic",
+                    title =          "Consistent and Elastic Registration of Histological Sections Using Vector-Spline Regularization",    
+                    publisher =  "Springer Berlin / Heidelberg",    
+                    booktitle =   "Computer Vision Approaches to Medical Image Analysis",
+                    series =       "Lecture Notes in Computer Science",
+                    year =          "2006",
+                    volume =      "4241",
+                    pages =       "85-95",
+                    month =       "May",
+                    city =            "Graz, Austria")
+            </citation>
+            <citation type="doi">10.1038/nmeth.2019</citation>
+        </citations>
+    </xml>
     <xml name="fiji_headless_citations">
         <citations>
             <citation type="doi">10.1038/nmeth.2102</citation>
         </citations>
     </xml>
-    <xml name="citations">
+    <xml name="bioformats_fiji_javabridge_citations">
         <citations>
             <citation type="doi">10.1038/nmeth.2102</citation>
             <citation type="doi">10.1038/nmeth.2019</citation>