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annotate scale_image.xml @ 2:f3c05a734dd1 draft

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
author imgteam
date Mon, 22 Jul 2019 05:04:55 -0400
parents 3e4231ed875e
children d09507d3fb0e
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f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
imgteam
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1 <tool id="ip_scale_image" name="Scale Image" version="0.4">
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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2 <description>Scales image</description>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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3 <requirements>
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f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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4 <requirement type="package" version="6.1.0">pillow</requirement>
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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5 <requirement type="package" version="0.14.2">scikit-image</requirement>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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6 <requirement type="package" version="1.15.4">numpy</requirement>
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f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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7 <requirement type="package" version="1.1.0">scipy</requirement>
f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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8 <requirement type="package" version="0.15.1">tifffile</requirement>
f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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9 </requirements>
f3c05a734dd1 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit b2acc1845a25828181597fe5b6982fe116a7796d
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10 <command detect_errors="aggressive">
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c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 <![CDATA[
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 python '$__tool_directory__/scale_image.py' '$input' ./out.png
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 #if $use_scale_option.use_scale == 'true'
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 $use_scale_option.scale
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 #else if $use_scale_option.use_scale == 'false'
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 '[$use_scale_option.scale_x, $use_scale_option.scale_y]'
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 #end if
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 $order
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 ]]>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 </command>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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22 <inputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <param name="input" type="data" format="png" label="Image file"/>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 <conditional name="use_scale_option"><!--a third option (using one integer as percentage scaling) could still be implemented-->
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <param label="Lock scaling between image dimensions" name="use_scale" type="select">
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <option selected="true" value="true">Lock</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <option value="false">Individual scales</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 </param>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <when value="true">
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <param name="scale" type="float" value="1.0" label="Scaling factor" />
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 </when>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <when value="false">
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 <param name="scale_x" type="integer" value="100" label="New height of the image in pixels" />
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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34 <param name="scale_y" type="integer" value="100" label="New width of the image in pixels" />
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 </when>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 </conditional>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 <param name="order" type="select" label="Interpolation method">
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <option value="0">Nearest-neighbor</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 <option value="1" selected="true">Bi-linear</option>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40 <option value="2">Bi-cubic</option>
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41 </param>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 </inputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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43 <outputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 <data format="png" name="output" from_work_dir="out.png"/>
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45 </outputs>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 <tests>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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47 <test>
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48 <param name="input" value="sample1.png"/> <!--continue here-->
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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49 <param name="use_scale_option.use_scale" value="false"/>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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50 <param name="use_scale_option.scale_x" value="200"/>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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51 <param name="use_scale_option.scale_y" value="150"/>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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52 <param name="order" value="0"/>
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53 <output name="output" value="out2.png" ftype="png" compare="sim_size"/>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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54 </test>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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55 </tests>
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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56 <help>
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57 **What it does**
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58
c4c76f1ebad2 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/scale_image/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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59 This tool scales an image using the scaling factor.
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60 </help>
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61 <citations>
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62 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation>
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63 </citations>
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64 </tool>