Mercurial > repos > iuc > imagej2_convert_format

annotate imagej2_convert_format.xml @ 5:a3806b0a32ed draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 378c3ecfbaed0330faf197811d379431b0f9e92c-dirty
author iuc
date Sun, 11 Oct 2015 13:30:31 -0400
parents 7a8b05b111f9
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
1 <?xml version='1.0' encoding='UTF-8'?>
4
7a8b05b111f9 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 3
diff changeset
2 <tool id="imagej2_convert_format" name="Convert image format" version="@WRAPPER_VERSION@.0">
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
3 <description>with bioformats</description>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
4 <macros>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
5 <import>imagej2_macros.xml</import>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
6 </macros>
4
7a8b05b111f9 planemo upload commit 18df9e67efd4adafcde4eb9b62cd815e4afe9733-dirty
iuc
parents: 3
diff changeset
7 <expand macro="python_bioformats_requirements" />
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
8 <command interpreter="python">
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
9 <![CDATA[
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
10 imagej2_convert_format.py
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
11 --in_fname "$input"
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
12 --input_datatype $input.ext
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
13 --output_datatype $output_datatype
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
14 --out_fname "$output"
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
15 ]]>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
16 </command>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
17 <inputs>
1
14d09b0ab9e1 planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
parents: 0
diff changeset
18 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
19 <param name="output_datatype" type="select" label="Convert to format">
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
20 <option value="jpg" selected="true">jpg</option>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
21 <option value="png">png</option>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
22 <option value="tiff">tiff</option>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
23 </param>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
24 </inputs>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
25 <outputs>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
26 <data name="output" format="jpg">
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
27 <actions>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
28 <action type="format">
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
29 <option type="from_param" name="output_datatype" />
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
30 </action>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
31 </actions>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
32 </data>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
33 </outputs>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
34 <tests>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
35 <test>
1
14d09b0ab9e1 planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
parents: 0
diff changeset
36 <param name="input" value="dot_blot.jpg" />
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
37 <param name="input_datatype" value="jpg" />
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
38 <param name="output_datatype" value="png" />
1
14d09b0ab9e1 planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
parents: 0
diff changeset
39 <output name="output" file="dot_blot.png" compare="sim_size" />
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
40 </test>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
41 <test>
1
14d09b0ab9e1 planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
parents: 0
diff changeset
42 <param name="input" value="dot_blot.png" />
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
43 <param name="input_datatype" value="png" />
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
44 <param name="output_datatype" value="tiff" />
1
14d09b0ab9e1 planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
parents: 0
diff changeset
45 <output name="output" file="dot_blot.tiff" compare="sim_size" />
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
46 </test>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
47 <test>
1
14d09b0ab9e1 planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
parents: 0
diff changeset
48 <param name="input" value="dot_blot.tiff" />
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
49 <param name="input_datatype" value="tiff" />
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
50 <param name="output_datatype" value="jpg" />
1
14d09b0ab9e1 planemo upload commit 7195716d447effc5bc32154279de4b84369eccdb-dirty
iuc
parents: 0
diff changeset
51 <output name="output" file="dot_blot.jpg" compare="sim_size" />
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
52 </test>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
53 </tests>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
54 <help>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
55 **What it does**
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
56
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
57 <![CDATA[
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
58 Converts an image file from one format to another where supported input and output formats are the
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
59 intersection of the relative formats supported by both Galaxy and Bioformats.
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
60
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
61 Go `here <https://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html>`_ for Bioformats image formats.
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
62 ]]>
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
63
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
64 </help>
2
cf9ed4ef641d planemo upload commit 369e40078146d00608d52205bb8cee66ae735b76-dirty
iuc
parents: 1
diff changeset
65 <expand macro="bioformats_fiji_javabridge_citations" />
0
312e8ce708b1 planemo upload commit 4bf97847c35c4dcf9638008b9b4b6c4e10015f19
iuc
parents:
diff changeset
66 </tool>