Mercurial > repos > iuc > modify_loom

annotate modify_loom.xml @ 2:9210c3553cdd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 5744259254d4254a29cb7a6687fbbfd103301064"
author iuc
date Wed, 05 Feb 2020 19:18:48 -0500
parents c8e4d0b9ae8c
children 05631436cdf1
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c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
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1 <tool id="modify_loom" name="Manipulate loom object" version="@VERSION@+@GALAXY_VERSION@">
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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2 <description>Add layers, or row/column attributes to a loom file</description>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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3 <macros>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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4 <import>macros.xml</import>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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5 </macros>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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6 <expand macro="requirements"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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7 <expand macro="version_command"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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8 <command detect_errors="exit_code"><![CDATA[
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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9 python '$__tool_directory__/modify_loom.py' -f '${input}'
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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10 #if $which_add.add_type == "cols":
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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11 -a cols -c '${which_add.cols}'
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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12 #else if $which_add.add_type == "cols":
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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13 -a rows -r '${which_add.rows}'
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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14 #else if $which_add.add_type == "layers":
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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15 -a layers -l '${which_add.layers}'
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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16 #end if
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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17 && cp '${input}' loom_add_out.loom
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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18 ]]></command>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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19 <inputs>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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20 <param name="input" type="data" format="loom" label="Loom file"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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21 <conditional name="which_add">
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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22 <param name="add_type" type="select" label="Select data attribute to add to loom">
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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23 <option value="cols">Columns</option>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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24 <option value="rows">Rows</option>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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25 <option value="layers">Layers</option>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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26 </param>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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27 <when value="cols">
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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28 <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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29 </when>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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30 <when value="rows">
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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31 <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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32 </when>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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33 <when value="layers">
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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34 <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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35 </when>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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36 </conditional>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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37 </inputs>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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38 <outputs>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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39 <data name="loomout" format="loom" from_work_dir='loom_add_out.loom' label="Expanded loom file from '${on_string}'"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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40 </outputs>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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41 <tests>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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42 <test expect_num_outputs="1">
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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43 <param name="input" value="addtest.loom"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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44 <param name="add_type" value="cols"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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45 <param name="cols" value="cols.tsv"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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46 <output name="loomout" value="addloomout1.loom" ftype="loom" compare="sim_size"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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47 </test>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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48 <test expect_num_outputs="1">
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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49 <param name="input" value="addtest.loom"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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50 <param name="add_type" value="rows"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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51 <param name="rows" value="rows.tsv"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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52 <output name="loomout" value="addloomout2.loom" ftype="loom" compare="sim_size"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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53 </test>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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54 <test expect_num_outputs="1">
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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55 <param name="input" value="addtest.loom"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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56 <param name="add_type" value="layers"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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57 <param name="layers" value="addlayer1.tsv"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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58 <output name="loomout" value="addloomout3.loom" ftype="loom" compare="sim_size"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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59 </test>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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60 </tests>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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61 <help><![CDATA[
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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62 This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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63 ]]></help>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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64 <citations>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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65 <citation type="bibtex">@UNPUBLISHED{Linnarsson2016,
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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66 author = "Linnarsson lab"
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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67 title = "Loompy"
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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68 year = "2013"
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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69 note = "https://github.com/linnarsson-lab/loompy"}
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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70 </citation>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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71 </citations>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
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72 </tool>