annotate imagej2_bunwarpj_compare_elastic_raw.xml @ 1:2be338fc671e draft default tip

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
author imgteam
date Mon, 28 Sep 2020 16:44:56 +0000
parents 1bffabc15695
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1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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1 <tool id="imagej2_bunwarpj_compare_elastic_raw" name="Compare elastic and raw deformation" version="@WRAPPER_VERSION@.0">
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2 <description>by warping index with bUnwarpJ</description>
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3 <macros>
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4 <import>imagej2_macros.xml</import>
1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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5 </macros>
1
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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6 <expand macro="fiji_requirements"/>
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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7 <command detect_errors="exit_code"><![CDATA[
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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8 #import os
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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9 #set output_log = 'output_log.txt'
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10 #set source_sans_ext = $os.path.splitext($os.path.basename($source_image.file_name))[0]
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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11 #set source_with_ext = '.'.join([source_sans_ext, $source_image.ext])
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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12 ln -s '$source_image.file_name' '$source_with_ext' &&
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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13 #set target_sans_ext = $os.path.splitext($os.path.basename($target_image.file_name))[0]
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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14 #set target_with_ext = '.'.join([target_sans_ext, $target_image.ext])
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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15 ln -s '$target_image.file_name' '$target_with_ext' &&
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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16 bunwarpj -compare_elastic_raw
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17 '$target_with_ext'
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18 '$source_with_ext'
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19 '$target_elastic_transformation'
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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20 '$source_raw_transformation'
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21 '$output'
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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22 &>'$output_log';
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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23 if [[ $? -ne 0 ]]; then
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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24 cat '$output_log' >&2;
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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25 else
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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26 grep -Po 'Warping index = \K[^ ]+' '$output_log' > '$output';
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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27 fi
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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28 ]]></command>
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29 <inputs>
1
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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30 <expand macro="param_target_image"/>
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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31 <expand macro="param_source_image"/>
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32 <param format="txt" name="target_elastic_transformation" type="data" label="Elastic transformation file"/>
1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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33 <param format="txt" name="source_raw_transformation" type="data" label="Raw transformation file"/>
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34 </inputs>
1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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35 <outputs>
1
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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36 <data name="output" format="txt" label="${tool.name} (same direction) on ${on_string}"/>
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37 </outputs>
1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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38 <tests>
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39 <test>
1
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40 <expand macro="test_target_source_images"/>
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41 <param name="target_elastic_transformation" value="target_elastic_transformation.txt"/>
2be338fc671e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit 2afb24f3c81d625312186750a714d702363012b5"
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42 <param name="source_raw_transformation" value="source_raw_transformation.txt"/>
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43 <output name="output" file="warping_index_raw.txt" compare="contains"/>
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44 </test>
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45 </tests>
1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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46 <help>
1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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47 **What it does**
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48
1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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49 <![CDATA[
1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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50 Calculates the warping index of an elastic transformation and a raw transformation. The elastic
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51 transformation file must be in the same format as the files created with the **Save transformation**
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52 option of the **Align two images with bUnwarpJ** tool, while the raw transformation file must be
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53 in the same format as the file produced by the **Convert elastic transformation to raw with bUnwarpJ**
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54 tool.
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55
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56 ]]>
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57
1bffabc15695 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/image_processing/imagej2 commit b08f0e6d1546caaf627b21f8c94044285d5d5b9c-dirty"
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58 </help>
1
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59 <expand macro="bunwarpj_citations"/>
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60 </tool>