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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
author imgteam
date Wed, 25 Sep 2024 16:16:58 +0000
parents 3d5f59603e13
children
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
imgteam
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1 <tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
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2 <description>with ImageJ2</description>
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3 <macros>
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4 <import>imagej2_macros.xml</import>
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5 </macros>
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6 <edam_operations>
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7 <edam_operation>operation_3443</edam_operation>
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8 </edam_operations>
3d5f59603e13 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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9 <xrefs>
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10 <xref type="bio.tools">imagej</xref>
3d5f59603e13 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
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11 <xref type="biii">imagej2</xref>
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12 </xrefs>
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13 <expand macro="fiji_requirements"/>
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14 <command detect_errors="exit_code"><![CDATA[
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15 #import os
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16 #set output_log = 'output_log.txt'
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17 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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18 #set source_with_ext = './' + '.'.join([source_sans_ext, $source_image.ext])
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19 ln -s '$source_image.file_name' '$source_with_ext' &&
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20 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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21 #set target_with_ext = './' + '.'.join([target_sans_ext, $target_image.ext])
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22 ln -s '$target_image.file_name' '$target_with_ext' &&
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23 bunwarpj -compare_elastic_raw
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24 '$target_with_ext'
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25 '$source_with_ext'
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26 '$target_elastic_transformation'
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27 '$source_raw_transformation'
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28 '$output'
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da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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29 2>&1 | tee '$output_log'
da91b5eaf92d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 8f49f3c66b5a1de99ec15e65c2519a56792f1d56
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30 && grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output'
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31 ]]></command>
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32 <inputs>
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33 <expand macro="param_target_image"/>
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34 <expand macro="param_source_image"/>
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35 <param format="txt" name="target_elastic_transformation" type="data" label="Elastic transformation file"/>
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36 <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file"/>
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37 </inputs>
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38 <outputs>
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39 <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}"/>
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40 </outputs>
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41 <tests>
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42 <test>
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43 <expand macro="test_target_source_images"/>
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44 <param name="target_elastic_transformation" value="target_elastic_transformation.txt"/>
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45 <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
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46 <output name="output" file="warping_index_raw.txt" compare="contains"/>
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47 </test>
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48 </tests>
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49 <help>
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50 **What it does**
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51
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52 <![CDATA[
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53 Calculates the warping index of an elastic transformation and a raw transformation. The elastic
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54 transformation file must be in the same format as the files created with the **Save transformation**
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55 option of the **Align two images with bUnwarpJ** tool, while the raw transformation file must be
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56 in the same format as the file produced by the **Convert elastic transformation to raw with bUnwarpJ**
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57 tool.
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59 ]]>
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61 </help>
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62 <expand macro="bunwarpj_citations"/>
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63 </tool>