Mercurial > repos > iuc > imagej2_convert_format

annotate imagej2_convert_format.xml @ 1:14d09b0ab9e1 draft

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author iuc
date Fri, 19 Jun 2015 16:59:08 -0400
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="imagej2_convert_format" name="Convert image format" version="1.0.0">
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3 <description>with bioformats</description>
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4 <macros>
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5 <import>imagej2_macros.xml</import>
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6 </macros>
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7 <expand macro="python_bioformats_requirements" />
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8 <command interpreter="python">
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9 <![CDATA[
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10 imagej2_convert_format.py
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11 --in_fname "$input"
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12 --input_datatype $input.ext
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13 --max_heap_size_type $set_max_heap_size.max_heap_size_type
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14 --max_heap_size $set_max_heap_size.max_heap_size
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15 --output_datatype $output_datatype
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16 --out_fname "$output"
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17 ]]>
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18 </command>
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19 <inputs>
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20 <expand macro="max_heap_size_type_conditional" />
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21 <param format="bmp,eps,gif,jpg,pcx,pgm,png,psd,tiff" name="input" type="data" label="Select image"/>
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22 <param name="output_datatype" type="select" label="Convert to format">
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23 <option value="jpg" selected="true">jpg</option>
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24 <option value="png">png</option>
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25 <option value="tiff">tiff</option>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data name="output" format="jpg">
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30 <actions>
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31 <action type="format">
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32 <option type="from_param" name="output_datatype" />
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33 </action>
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34 </actions>
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35 </data>
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36 </outputs>
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37 <tests>
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38 <test>
1
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39 <param name="input" value="dot_blot.jpg" />
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40 <param name="input_datatype" value="jpg" />
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41 <param name="output_datatype" value="png" />
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42 <output name="output" file="dot_blot.png" compare="sim_size" />
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43 </test>
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44 <test>
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45 <param name="input" value="dot_blot.png" />
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46 <param name="input_datatype" value="png" />
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47 <param name="output_datatype" value="tiff" />
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48 <output name="output" file="dot_blot.tiff" compare="sim_size" />
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49 </test>
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50 <test>
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51 <param name="input" value="dot_blot.tiff" />
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52 <param name="input_datatype" value="tiff" />
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53 <param name="output_datatype" value="jpg" />
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54 <output name="output" file="dot_blot.jpg" compare="sim_size" />
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55 </test>
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56 </tests>
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57 <help>
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58 **What it does**
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59
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60 <![CDATA[
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61 Converts an image file from one format to another where supported input and output formats are the
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62 intersection of the relative formats supported by both Galaxy and Bioformats.
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63
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64 Go `here <https://www.openmicroscopy.org/site/support/bio-formats5.1/supported-formats.html>`_ for Bioformats image formats.
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65 ]]>
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66
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67 </help>
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68 <expand macro="citations" />
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69 </tool>