Mercurial > repos > iuc > imagej2_convert_format

changeset 1:14d09b0ab9e1 draft

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planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
author iuc
date Fri, 19 Jun 2015 16:59:08 -0400
parents 312e8ce708b1
children cf9ed4ef641d
files imagej2_convert_format.py imagej2_convert_format.xml tool_dependencies.xml
diffstat 3 files changed, 8 insertions(+), 14 deletions(-) [+]
line wrap: on
line diff
--- a/imagej2_convert_format.py	Tue Jun 09 12:21:40 2015 -0400
+++ b/imagej2_convert_format.py	Fri Jun 19 16:59:08 2015 -0400
@@ -1,8 +1,4 @@
 #!/usr/bin/env python
-# Galaxy wrapper for use with Imagej2 via bioformats and javabridge by Greg Von Kuster
-"""
-A wrapper script for running ImageJ2 commands via bioformats and javabridge.
-"""
 import argparse
 import imagej2_base_utils
 import imagej2_utils
--- a/imagej2_convert_format.xml	Tue Jun 09 12:21:40 2015 -0400
+++ b/imagej2_convert_format.xml	Fri Jun 19 16:59:08 2015 -0400
@@ -18,7 +18,7 @@
     </command>
     <inputs>
         <expand macro="max_heap_size_type_conditional" />
-        <param format="bmp,eps,gif,html,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
+        <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
         <param name="output_datatype" type="select" label="Convert to format">
             <option value="jpg" selected="true">jpg</option>
             <option value="png">png</option>
@@ -36,24 +36,22 @@
     </outputs>
     <tests>
         <test>
-            <param name="input" value="dot_blot.jpg" ftype="jpg" />
-            <param name="max_heap_size_type" value="megabytes" />
-            <param name="max_heap_size" value="256" />
+            <param name="input" value="dot_blot.jpg" />
             <param name="input_datatype" value="jpg" />
             <param name="output_datatype" value="png" />
-            <output name="output" file="dot_blot.png" ftype="png" />
+            <output name="output" file="dot_blot.png" compare="sim_size" />
         </test>
         <test>
-            <param name="input" value="dot_blot.png" ftype="png" />
+            <param name="input" value="dot_blot.png" />
             <param name="input_datatype" value="png" />
             <param name="output_datatype" value="tiff" />
-            <output name="output" file="dot_blot.tiff" ftype="tiff" />
+            <output name="output" file="dot_blot.tiff" compare="sim_size" />
         </test>
         <test>
-            <param name="input" value="dot_blot.tiff" ftype="tiff" />
+            <param name="input" value="dot_blot.tiff" />
             <param name="input_datatype" value="tiff" />
             <param name="output_datatype" value="jpg" />
-            <output name="output" file="dot_blot.jpg" ftype="jpg" />
+            <output name="output" file="dot_blot.jpg" compare="sim_size" />
         </test>
     </tests>
     <help>
--- a/tool_dependencies.xml	Tue Jun 09 12:21:40 2015 -0400
+++ b/tool_dependencies.xml	Fri Jun 19 16:59:08 2015 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="fiji" version="20141125">
-        <repository changeset_revision="2957c52b8fe0" name="package_fiji_20141125" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="7121a1ea4839" name="package_fiji_20141125" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="javabridge" version="1.0.11">
         <repository changeset_revision="8d338153c3dc" name="package_javabridge_1_0_11" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />