diff imagej2_macros.xml @ 0:bb84f130a4e1 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imagej2_macros.xml	Tue Sep 17 17:04:59 2019 -0400
@@ -0,0 +1,106 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <token name="@WRAPPER_VERSION@">3.0</token>
+    <xml name="fiji_requirements">
+        <requirements>
+            <requirement type="package" version="20170530">fiji</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:"/>
+            <exit_code range=":-1"/>
+            <regex match="Error:"/>
+            <regex match="Exception:"/>
+        </stdio>
+    </xml>
+    <xml name="image_type">
+        <param name="image_type" type="select" label="Image type">
+            <option value="8-bit_white" selected="True">8-bit white</option>
+            <option value="8-bit_black">8-bit black</option>
+            <option value="8-bit_random">8-bit random</option>
+            <option value="8-bit_ramp">8-bit ramp</option>
+            <option value="16-bit_white">16-bit white</option>
+            <option value="16-bit_black">16-bit black</option>
+            <option value="16-bit_random">16-bit random</option>
+            <option value="16-bit_ramp">16-bit ramp</option>
+            <option value="32-bit_white">32-bit white</option>
+            <option value="32-bit_black">32-bit black</option>
+            <option value="32-bit_random">32-bit random</option>
+            <option value="32-bit_ramp">32-bit ramp</option>
+            <option value="RGB_white">RGB white</option>
+            <option value="RGB_black">RGB black</option>
+            <option value="RGB_random">RGB random</option>
+            <option value="RGB_ramp">RGB ramp</option>
+        </param>
+    </xml>
+    <xml name="make_binary_params">
+        <param name="iterations" type="integer" value="1" min="1" max="100" label="Iterations" help="The number of times (1-100) erosion, dilation, opening, and closing are performed."/>
+        <param name="count" type="integer" value="1" min="1" max="8" label="Count" help="The number of adjacent background pixels necessary (1-8) for erosion or dilation."/>
+        <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite).">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+        </param>
+        <param name="pad_edges_when_eroding" type="select" label="Pad edges when eroding" help="If Yes, eroding does not erode from the edges of the image.">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+        </param>
+    </xml>
+    <xml name="black_background_param">
+        <param name="black_background" type="select" label="Black background" help="If Yes, the background is black and the foreground is white (no implies the opposite).">
+            <option value="no" selected="True">No</option>
+            <option value="yes">Yes</option>
+        </param>
+    </xml>
+    <token name="@make_binary_args@">
+        --iterations $iterations
+        --count $count
+        --black_background $black_background
+        --pad_edges_when_eroding $pad_edges_when_eroding
+    </token>
+    <token name="@requires_binary_input@">
+.. class:: warningmark
+
+This tool works on binary images, so other image types will automatically be converted to binary
+before they are analyzed.  This step is performed using the ImageJ2 **Make Binary** command with
+the following settings: **Iterations:** 1, **Count:** 1, **Pad edges when eroding:** No.  The tool
+allows you to choose the **Black background** setting.  If these settings are not appropriate,
+first manually convert the image to binary using the **Convert to binary (black and white)**
+tool, which allows you to change them.
+    </token>
+    <xml name="image_datatypes">
+        <option value="bmp">bmp</option>
+        <option value="gif">gif</option>
+        <option value="jpg">jpg</option>
+        <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>
+</macros>