Mercurial > repos > imgteam > 2d_simple_filter
annotate filter.xml @ 2:f70b215d155c draft
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
author | imgteam |
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date | Fri, 10 Nov 2023 13:44:57 +0000 |
parents | dba87c4b32d3 |
children | 6c4b22ef2b81 |
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f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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1 <tool id="ip_filter_standard" name="Filter 2D image" version="0.0.3-3"> |
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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2 <description>with scikit-image</description> |
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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3 <edam_operations> |
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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4 <edam_operation>operation_3443</edam_operation> |
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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5 </edam_operations> |
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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6 <xrefs> |
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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7 <xref type="bio.tools">scikit-image</xref> |
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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8 <xref type="biii">scikit-image</xref> |
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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9 </xrefs> |
0
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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10 <requirements> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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11 <requirement type="package" version="0.14.2">scikit-image</requirement> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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12 <requirement type="package" version="1.15.4">numpy</requirement> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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13 <requirement type="package" version="5.3.0">pillow</requirement> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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14 <requirement type="package" version="0.15.1">tifffile</requirement> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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15 </requirements> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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16 <command detect_errors="aggressive"> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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17 <![CDATA[ |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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18 python '$__tool_directory__/filter_image.py' '$input' '$output' $filter_type $radius |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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19 ]]> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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20 </command> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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21 <inputs> |
2
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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22 <param name="filter_type" type="select" label="Filter type"> |
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f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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23 <option value="median" selected="True">Median</option> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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24 <option value="gaussian">Gaussian Blur</option> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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25 <option value="prewitt">Prewitt</option> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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26 <option value="sobel">Sobel</option> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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27 <option value="scharr">Scharr</option> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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28 </param> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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29 <param name="radius" type="integer" value="3" label="Radius/Sigma" /> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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30 <param name="input" type="data" format="tiff" label="Source file" /> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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31 </inputs> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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32 <outputs> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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33 <data format="tiff" name="output" /> |
2
f70b215d155c
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_simple_filter/ commit 56e3f647d08d5e6c973d5e6cd89bb677db6473ab
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34 </outputs> |
0
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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35 <tests> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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36 <test> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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37 <param name="input" value="sample.tif" /> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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38 <output name="output" value="res.tif" ftype="tiff" compare="sim_size"/> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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39 <param name="filter_type" value="prewitt" /> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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40 <param name="radius" value="4" /> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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41 </test> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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42 </tests> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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43 <help> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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44 **What it does** |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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45 |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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46 Applies a standard filter to an image. |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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47 </help> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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48 <citations> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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49 <citation type="doi">10.1016/j.jbiotec.2017.07.019</citation> |
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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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50 </citations> |
f264ae82f735
planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_simple_filter/ commit c3f4b766f03770f094fda6bda0a5882c0ebd4581
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51 </tool> |