Mercurial > repos > iuc > anndata_manipulate
annotate manipulate.xml @ 14:c4209ea387d4 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit c1d84c1850c53deccc384de3960d2cec37bb2869
| author | iuc |
|---|---|
| date | Fri, 08 Nov 2024 21:59:34 +0000 |
| parents | 7e8c677a7b71 |
| children |
| rev | line source |
|---|---|
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
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changeset
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1 <tool id="anndata_manipulate" name="Manipulate AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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2 <description>object</description> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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changeset
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3 <macros> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
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4 <import>macros.xml</import> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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5 <xml name="param_join"> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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6 <param name="join" type="select" label="The connecting string between name and integer"> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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7 <option value="-">-</option> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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8 <option value="_">_</option> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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9 <option value=" "> </option> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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10 <option value="/">/</option> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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11 </param> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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changeset
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12 </xml> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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13 </macros> |
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14
c4209ea387d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit c1d84c1850c53deccc384de3960d2cec37bb2869
iuc
parents:
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14 <expand macro="bio_tools"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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15 <expand macro="requirements"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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16 <expand macro="version_command"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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17 <command detect_errors="exit_code"><![CDATA[ |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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18 @CMD@ |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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19 ]]></command> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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20 <configfiles> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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21 <configfile name="script_file"><![CDATA[ |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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22 @CMD_imports@ |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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23 |
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ed4996a16f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
iuc
parents:
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24 adata = ad.read_h5ad('$input') |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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25 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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26 #if $manipulate.function == 'concatenate' |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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27 #for i, filepath in enumerate($manipulate.other_adatas) |
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ed4996a16f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
iuc
parents:
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28 adata_$i = ad.read_h5ad('$filepath') |
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0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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29 #end for |
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7
43cb7b5a6fe7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2"
iuc
parents:
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30 adata = adata.concatenate( |
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0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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31 #for i, filepath in enumerate($manipulate.other_adatas) |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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changeset
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32 adata_$i, |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
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33 #end for |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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changeset
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34 join='$manipulate.join', |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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35 #if str($manipulate.index_unique) != '' |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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36 index_unique='$manipulate.index_unique', |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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37 #else |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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38 index_unique=None, |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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39 #end if |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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40 batch_key='$manipulate.batch_key') |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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41 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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42 #else if $manipulate.function == 'var_names_make_unique' |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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43 adata.var_names_make_unique(join='$manipulate.join') |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
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44 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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45 #else if $manipulate.function == 'obs_names_make_unique' |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
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46 adata.obs_names_make_unique(join='$manipulate.join') |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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47 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
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48 #else if $manipulate.function == 'rename_categories' |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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49 #set $categories = [x.strip() for x in str($manipulate.categories).split(',')] |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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50 adata.rename_categories( |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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51 key='$manipulate.key', |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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52 categories=$categories) |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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53 |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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54 #else if $manipulate.function == 'remove_keys' |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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55 #if $manipulate.obs_keys |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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56 #set $keys = [x.strip() for x in str($manipulate.obs_keys).split(',')] |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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57 adata.obs = adata.obs.drop(columns=$keys) |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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58 #end if |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
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59 |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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60 #if $manipulate.var_keys |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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61 #set $keys = [x.strip() for x in str($manipulate.var_keys).split(',')] |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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62 adata.var = adata.vars.drop(columns=$keys) |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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63 #end if |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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64 |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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65 #else if $manipulate.function == 'flag_genes' |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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66 ## adapted from anndata operations |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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67 #for $flag in $manipulate.gene_flags |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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68 k_cat = adata.var_names.str.startswith('${flag.startswith}') |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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69 if k_cat.sum() > 0: |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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70 adata.var['${flag.col_name}'] = k_cat |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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71 else: |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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72 print(f'No genes starting with {'${flag.startswith}'} found.') |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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73 #end for |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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74 |
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0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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75 #else if $manipulate.function == 'strings_to_categoricals' |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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76 adata.strings_to_categoricals() |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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77 |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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78 #else if $manipulate.function == 'transpose' |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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79 adata = adata.transpose() |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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80 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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81 #else if $manipulate.function == 'add_annotation' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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82 import pandas as pd |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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83 extra_annot_t = pd.read_csv('$manipulate.new_annot', sep='\t').reset_index(drop=True) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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84 #if $manipulate.var_obs == 'var' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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85 var_index = adata.var_names |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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86 var = pd.concat([adata.var.reset_index(drop=True), extra_annot_t], axis=1) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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87 var.index = var_index |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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88 adata.var = var |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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89 #else if $manipulate.var_obs == 'obs' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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90 obs_index = adata.obs.index |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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91 obs = pd.concat([adata.obs.reset_index(drop=True), extra_annot_t], axis=1) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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92 obs.index = obs_index |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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93 adata.obs = obs |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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94 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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95 |
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13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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96 #else if $manipulate.function == 'split_on_obs' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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97 import os |
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98 res_dir = "output_split" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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99 os.makedirs(res_dir, exist_ok=True) |
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100 for s,field_value in enumerate(adata.obs["${manipulate.key}"].unique()): |
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101 ad_s = adata[adata.obs.${manipulate.key} == field_value] |
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102 ad_s.write(f"{res_dir}/${manipulate.key}_{s}.h5ad", compression='gzip') |
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103 |
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1
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104 #else if $manipulate.function == 'filter' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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105 #if $manipulate.filter.filter == 'key' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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106 #if $manipulate.var_obs == 'var' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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107 filtered = adata.var['$manipulate.filter.key'] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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108 #else if $manipulate.var_obs == 'obs' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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109 filtered = adata.obs['$manipulate.filter.key'] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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110 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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111 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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112 #if $manipulate.filter.filter_key.type == 'number' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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113 #if $manipulate.filter.filter_key.filter == 'equal' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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114 filtered = filtered == $manipulate.filter.filter_key.value |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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115 #else if $manipulate.filter.filter_key.filter == 'equal' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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116 filtered = filtered != $manipulate.filter.filter_key.value |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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117 #else if $manipulate.filter.filter_key.filter == 'less' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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118 filtered = filtered < $manipulate.filter.filter_key.value |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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119 #else if $manipulate.filter.filter_key.filter == 'less_or_equal' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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120 filtered = filtered <= $manipulate.filter.filter_key.value |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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121 #else if $manipulate.filter.filter_key.filter == 'greater' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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122 filtered = filtered > $manipulate.filter.filter_key.value |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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123 #else if $manipulate.filter.filter_key.filter == 'greater_or_equal' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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124 filtered = filtered >= $manipulate.filter.filter_key.value |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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125 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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126 #else if $manipulate.filter.filter_key.type == 'text' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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127 #if $manipulate.filter.filter_key.filter == 'equal' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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128 filtered = filtered == '$manipulate.filter.filter_key.value' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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129 #else |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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130 filtered = filtered != '$manipulate.filter.filter_key.value' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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131 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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132 #else if $manipulate.filter.filter_key.type == 'boolean' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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133 filtered = filtered == $manipulate.filter.filter_key.value |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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134 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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135 |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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136 #else if $manipulate.filter.filter == 'index' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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137 #if str($manipulate.filter.index.format) == 'file' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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138 with open('$manipulate.filter.index.file', 'r') as filter_f: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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139 filters = [str(x.strip()) for x in filter_f.readlines()] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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140 filtered = filters |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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141 #else |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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142 #set $filters = [str(x.strip()) for x in $manipulate.filter.index.text.split(',')] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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143 filtered = $filters |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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144 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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145 #end if |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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146 print(filtered) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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147 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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148 #if $manipulate.var_obs == 'var' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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149 adata = adata[:,filtered] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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150 #else if $manipulate.var_obs == 'obs' |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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151 adata = adata[filtered, :] |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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152 #end if |
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2
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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153 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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154 #else if $manipulate.function == 'save_raw' |
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a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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155 adata.raw = adata |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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156 |
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157 #end if |
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158 |
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159 #if $manipulate.function != 'split_on_obs' |
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160 adata.write('anndata.h5ad', compression='gzip') |
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161 print(adata) |
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162 #end if |
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163 |
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164 ]]></configfile> |
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165 </configfiles> |
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166 <inputs> |
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167 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/> |
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168 <conditional name="manipulate"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6b5d0d6f038ebd0fae5dbca02ada51555518ed85"
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169 <param name="function" type="select" label="Function to manipulate the object"> |
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170 <option value="concatenate">Concatenate along the observations axis</option> |
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171 <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option> |
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172 <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option> |
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173 <option value="rename_categories">Rename categories of annotation</option> |
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174 <option value="remove_keys">Remove keys from obs or var annotations</option> |
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175 <option value="flag_genes">Flag genes start with a pattern</option><!--adapted from EBI anndata operations tool --> |
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176 <option value="strings_to_categoricals">Transform string annotations to categoricals</option> |
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177 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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178 <option value="add_annotation">Add new annotation(s) for observations or variables</option> |
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179 <option value="split_on_obs">Split the AnnData object into multiple AnnData objects based on the values of a given obs key</option><!--adapted from EBI anndata operations tool--> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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180 <option value="filter">Filter observations or variables</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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181 <option value="save_raw">Freeze the current state into the 'raw' attribute</option> |
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182 </param> |
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183 <when value="concatenate"> |
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184 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/> |
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185 <param name="join" type="select" label="Join method"> |
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186 <option value="inner">Intersection of variables</option> |
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187 <option value="outer">Union of variables</option> |
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188 </param> |
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189 <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/> |
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190 <param name="index_unique" type="select" label="Separator to join the existing index names with the batch category" help="Leave it empty to keep existing indices"> |
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191 <option value="-">-</option> |
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192 <option value="_">_</option> |
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193 <option value=" "> </option> |
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194 <option value="/">/</option> |
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195 </param> |
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196 </when> |
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197 <when value="obs_names_make_unique"> |
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198 <expand macro="param_join"/> |
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199 </when> |
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200 <when value="var_names_make_unique"> |
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201 <expand macro="param_join"/> |
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202 </when> |
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203 <when value="rename_categories"> |
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204 <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/> |
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205 <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/> |
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206 </when> |
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207 <when value="remove_keys"> |
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208 <param name="obs_keys" type="text" value="" optional="true" label="Keys/fields to remove from observations (obs)"> |
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209 <expand macro="sanitize_query"/> |
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210 </param> |
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211 <param name="var_keys" type="text" value="" optional="true" label="Keys/fields to remove from variables (var)"> |
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212 <expand macro="sanitize_query"/> |
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213 </param> |
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214 </when> |
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215 <when value="flag_genes"> |
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216 <repeat name="gene_flags" title="Flag genes that start with these names"> |
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217 <param name="startswith" type="text" label="Text that you expect the genes to be flagged to start with" help="For example, 'MT-' for mito genes"> |
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218 <sanitizer invalid_char=""> |
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219 <valid initial="string.ascii_letters,string.digits,string.punctuation"> |
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220 <remove value="'" /> |
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221 </valid> |
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222 </sanitizer> |
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223 </param> |
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224 <param name="col_name" type="text" label="Name of the column in var.names where this boolean flag is stored" help="For example, name this column as 'mito' for mitochondrial genes."/> |
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225 </repeat> |
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226 </when> |
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7
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2"
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227 <when value="strings_to_categoricals" ></when> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2"
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228 <when value="transpose" ></when> |
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1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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229 <when value="add_annotation"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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230 <param name="var_obs" type="select" label="What to annotate?"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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231 <option value="var">Variables (var)</option> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
232 <option value="obs">Observations (obs)</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
233 </param> |
|
12
ed4996a16f7f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 656ce7ff596a8870b77848469e85b406c7bd9344
iuc
parents:
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diff
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|
234 <param name="new_annot" type="data" format="tabular" label="Table with new annotations" |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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0
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|
235 help="The new table should have the same number of rows and same order than obs or var. The key names should be in the header (1st line)"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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|
236 </when> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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237 <when value="split_on_obs"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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238 <param name="key" type="text" label="The obs key to split on" help="For example, if you want to split on cluster annotation, you can use the key 'louvain'. The output will be a collection of anndata objects"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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diff
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239 <sanitizer invalid_char=""> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
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240 <valid initial="string.ascii_letters,string.digits,string.punctuation"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
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241 <remove value="'" /> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
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242 </valid> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
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243 </sanitizer> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
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|
244 </param> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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245 </when> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
246 <when value="filter"> |
|
2
a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
1
diff
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247 <param name="var_obs" type="select" label="What to filter?"> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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changeset
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248 <option value="var">Variables (var)</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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changeset
|
249 <option value="obs">Observations (obs)</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
250 </param> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
251 <conditional name="filter"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
252 <param name="filter" type="select" label="Type of filtering?"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
253 <option value="key">By key (column) values</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
254 <option value="index">By index (row)</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
255 </param> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
256 <when value="key"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
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|
257 <param name="key" type="text" value="n_genes" label="Key to filter"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
258 <conditional name="filter_key"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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changeset
|
259 <param name="type" type="select" label="Type of value to filter"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
changeset
|
260 <option value="number">Number</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
changeset
|
261 <option value="text">Text</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
262 <option value="boolean">Boolean</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
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263 </param> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
264 <when value="number"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
265 <param name="filter" type="select" label="Filter"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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diff
changeset
|
266 <option value="equal">equal to</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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changeset
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267 <option value="not_equal">not equal to</option> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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268 <option value="less">less than</option> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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269 <option value="less_or_equal">less than or equal to</option> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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changeset
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270 <option value="greater">greater than</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
271 <option value="greater_or_equal">greater than or equal to</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
272 </param> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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273 <param name="value" type="float" value="2500" label="Value"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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274 </when> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
275 <when value="text"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
276 <param name="filter" type="select" label="Filter"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
277 <option value="equal">equal to</option> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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278 <option value="not_equal">not equal to</option></param> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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279 <param name="value" type="text" value="2500" label="Value"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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280 </when> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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281 <when value="boolean"> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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282 <param name="value" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Value to keep"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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283 </when> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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284 </conditional> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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285 </when> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
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286 <when value="index"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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287 <conditional name="index"> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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changeset
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288 <param name="format" type="select" label="Format for the filter by index"> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
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289 <option value="file">File</option> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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290 <option value="text" selected="true">Text</option> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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291 </param> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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292 <when value="text"> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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293 <param name="text" type="text" value="" label="List of index to keep" help="Indexes separated by a comma"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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294 </when> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
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295 <when value="file"> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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296 <param name="file" type="data" format="txt" label="File with the list of index to keep" help="One index per line"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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297 </when> |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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298 </conditional> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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299 </when> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
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|
300 </conditional> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
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301 </when> |
|
7
43cb7b5a6fe7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 033c2d20a0c73cd84c5c3aee73ae224183a9c1c2"
iuc
parents:
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302 <when value="save_raw"></when> |
|
0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
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303 </conditional> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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304 </inputs> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
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305 <outputs> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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306 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${manipulate.function}) on ${on_string}"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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307 <filter>manipulate['function'] != 'split_on_obs'</filter> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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308 </data> |
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309 <collection name="output_h5ad_split" type="list" label="${tool.name} (${manipulate.function}) on ${on_string} Collection"> |
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310 <discover_datasets pattern="(?P<designation>.+)\.h5" directory="output_split" format="h5ad" visible="true"/> |
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311 <filter>manipulate['function'] == 'split_on_obs'</filter> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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312 </collection> |
|
0
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313 </outputs> |
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314 <tests> |
|
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315 <test expect_num_outputs="1"> |
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1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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316 <!-- test 1 --> |
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8
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 6497f5415b57bedd849b876883574b3f0050741a"
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317 <param name="input" value="import.csv.h5ad"/> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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318 <conditional name="manipulate"> |
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319 <param name="function" value="concatenate"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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320 <param name="other_adatas" value="import.csv.h5ad"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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321 <param name="join" value="inner"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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322 <param name="batch_key" value="batch"/> |
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0ef28c0963c8
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323 <param name="index_unique" value="-"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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324 </conditional> |
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325 <assert_stdout> |
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326 <has_text_matching expression="adata_0"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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327 <has_text_matching expression="adata.concatenate"/> |
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0ef28c0963c8
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328 <has_text_matching expression="join='inner'"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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329 <has_text_matching expression="index_unique='-'"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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330 <has_text_matching expression="batch_key='batch'"/> |
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13
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331 <has_text_matching expression="6 × 2"/> |
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0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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332 </assert_stdout> |
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13
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333 <output name="anndata" ftype="h5ad"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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334 <assert_contents> |
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335 <has_h5_keys keys="obs/batch"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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336 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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337 </output> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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338 </test> |
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13
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339 <test expect_num_outputs="1"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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340 <!-- test 2 --> |
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0
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341 <param name="input" value="krumsiek11.h5ad"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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342 <conditional name="manipulate"> |
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343 <param name="function" value="obs_names_make_unique"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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344 <param name="join" value="-"/> |
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345 </conditional> |
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346 <assert_stdout> |
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347 <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/> |
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348 <has_text_matching expression="500 × 11"/> |
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0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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349 </assert_stdout> |
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13
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350 <output name="anndata" ftype="h5ad"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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351 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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352 <has_h5_keys keys="obs/cell_type"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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353 <has_h5_keys keys="uns/highlights"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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354 <has_h5_keys keys="uns/iroot"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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355 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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356 </output> |
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0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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357 </test> |
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13
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358 <test expect_num_outputs="1"> |
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1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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359 <!-- test 3 --> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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360 <param name="input" value="krumsiek11.h5ad"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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361 <conditional name="manipulate"> |
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0ef28c0963c8
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362 <param name="function" value="var_names_make_unique"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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363 <param name="join" value="-"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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364 </conditional> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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365 <assert_stdout> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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366 <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/> |
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13
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367 <has_text_matching expression="500 × 11"/> |
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0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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368 </assert_stdout> |
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13
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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369 <output name="anndata" ftype="h5ad"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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370 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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371 <has_h5_keys keys="obs/cell_type"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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372 <has_h5_keys keys="uns/highlights"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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373 <has_h5_keys keys="uns/iroot"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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374 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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375 </output> |
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0
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376 </test> |
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13
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377 <test expect_num_outputs="1"> |
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1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
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378 <!-- test 4 --> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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379 <param name="input" value="krumsiek11.h5ad"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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changeset
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380 <conditional name="manipulate"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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381 <param name="function" value="rename_categories"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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382 <param name="key" value="cell_type"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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383 <param name="categories" value="ery, mk, mo, progenitor"/> |
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0
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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384 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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385 <assert_stdout> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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386 <has_text_matching expression="adata.rename_categories"/> |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
387 <has_text_matching expression="key='cell_type'"/> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
388 <has_text_matching expression="categories=\['ery', 'mk', 'mo', 'progenitor'\]"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
389 <has_text_matching expression="500 × 11"/> |
|
0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
390 </assert_stdout> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
391 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
392 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
393 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
394 <has_h5_keys keys="uns/highlights"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
395 <has_h5_keys keys="uns/iroot"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
396 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
397 </output> |
|
0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
398 </test> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
399 <test expect_num_outputs="1"> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
400 <!-- test 5 --> |
|
0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
401 <param name="input" value="krumsiek11.h5ad"/> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
402 <conditional name="manipulate"> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
403 <param name="function" value="strings_to_categoricals"/> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
404 </conditional> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
405 <assert_stdout> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
406 <has_text_matching expression="adata.strings_to_categoricals"/> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
407 <has_text_matching expression="500 × 11"/> |
|
0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
408 </assert_stdout> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
409 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
410 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
411 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
412 <has_h5_keys keys="uns/highlights"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
413 <has_h5_keys keys="uns/iroot"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
414 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
415 </output> |
|
0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
416 </test> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
417 <test expect_num_outputs="1"> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
418 <!-- test 6 --> |
|
0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
419 <param name="input" value="krumsiek11.h5ad"/> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
420 <conditional name="manipulate"> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
421 <param name="function" value="transpose"/> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
422 </conditional> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
423 <assert_stdout> |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
424 <has_text_matching expression="adata.transpose"/> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
425 <has_text_matching expression="11 × 500"/> |
|
0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
426 </assert_stdout> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
427 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
428 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
429 <has_h5_keys keys="var/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
430 <has_h5_keys keys="uns/highlights"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
431 <has_h5_keys keys="uns/iroot"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
432 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
433 </output> |
|
0
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
parents:
diff
changeset
|
434 </test> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
435 <test expect_num_outputs="1"> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
436 <!-- test 7 --> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
437 <param name="input" value="krumsiek11.h5ad"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
438 <conditional name="manipulate"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
439 <param name="function" value="add_annotation"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
440 <param name="var_obs" value="var"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
441 <param name="new_annot" value="var_add_annotation.tabular"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
442 </conditional> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
443 <assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
444 <has_text_matching expression="500 × 11"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
445 </assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
446 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
447 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
448 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
449 <has_h5_keys keys="var/annot1"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
450 <has_h5_keys keys="var/annot2"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
451 <has_h5_keys keys="uns/highlights"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
452 <has_h5_keys keys="uns/iroot"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
453 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
454 </output> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
455 </test> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
456 <test expect_num_outputs="1"> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
457 <!-- test 8 --> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
458 <param name="input" value="krumsiek11.h5ad"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
459 <conditional name="manipulate"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
460 <param name="function" value="add_annotation"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
461 <param name="var_obs" value="obs"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
462 <param name="new_annot" value="obs_add_annotation.tabular"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
463 </conditional> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
464 <assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
465 <has_text_matching expression="500 × 11"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
466 </assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
467 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
468 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
469 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
470 <has_h5_keys keys="obs/annot1"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
471 <has_h5_keys keys="obs/annot2"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
472 <has_h5_keys keys="uns/highlights"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
473 <has_h5_keys keys="uns/iroot"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
474 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
475 </output> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
476 </test> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
477 <test expect_num_outputs="1"> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
478 <!-- test 9 --> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
479 <param name="input" value="krumsiek11.h5ad"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
480 <conditional name="manipulate"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
481 <param name="function" value="filter"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
482 <param name="var_obs" value="var"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
483 <conditional name="filter"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
484 <param name="filter" value="index"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
485 <conditional name="index"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
486 <param name="format" value="text"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
487 <param name="text" value="Gata2,EKLF"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
488 </conditional> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
489 </conditional> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
490 </conditional> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
491 <assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
492 <has_text_matching expression="500 × 2"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
493 </assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
494 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
495 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
496 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
497 <has_h5_keys keys="uns/highlights"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
498 <has_h5_keys keys="uns/iroot"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
499 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
500 </output> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
501 </test> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
502 <test expect_num_outputs="1"> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
503 <!-- test 10 --> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
504 <param name="input" value="krumsiek11.h5ad"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
505 <conditional name="manipulate"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
506 <param name="function" value="filter"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
507 <param name="var_obs" value="obs"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
508 <conditional name="filter"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
509 <param name="filter" value="key"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
510 <param name="key" value="cell_type"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
511 <conditional name="filter_key"> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
512 <param name="type" value="text"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
513 <param name="filter" value="equal"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
514 <param name="value" value="progenitor"/> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
515 </conditional> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
516 </conditional> |
|
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
517 </conditional> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
518 <assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
519 <has_text_matching expression="260 × 11"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
520 </assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
521 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
522 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
523 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
524 <has_h5_keys keys="uns/highlights"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
525 <has_h5_keys keys="uns/iroot"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
526 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
527 </output> |
|
1
19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
iuc
parents:
0
diff
changeset
|
528 </test> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
529 <test expect_num_outputs="1"> |
|
2
a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
1
diff
changeset
|
530 <!-- test 11 --> |
|
a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
1
diff
changeset
|
531 <param name="input" value="krumsiek11.h5ad"/> |
|
a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
1
diff
changeset
|
532 <conditional name="manipulate"> |
|
a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
1
diff
changeset
|
533 <param name="function" value="save_raw"/> |
|
a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
iuc
parents:
1
diff
changeset
|
534 </conditional> |
|
13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
535 <assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
536 <has_text_matching expression="500 × 11"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
537 </assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
538 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
539 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
540 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
541 <has_h5_keys keys="uns/highlights"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
542 <has_h5_keys keys="uns/iroot"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
543 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
544 </output> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
545 </test> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
546 <test expect_num_outputs="1"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
547 <!-- test 12 remove_keys --> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
548 <param name="input" value="krumsiek11.h5ad"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
549 <conditional name="manipulate"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
550 <param name="function" value="remove_keys"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
551 <param name="obs_keys" value="cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
552 </conditional> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
553 <assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
554 <has_text_matching expression="500 × 11"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
555 </assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
556 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
557 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
558 <has_h5_keys keys="uns/highlights"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
559 <has_h5_keys keys="uns/iroot"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
560 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
561 </output> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
562 </test> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
563 <test expect_num_outputs="1"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
564 <!-- test 13 flag_genes --> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
565 <param name="input" value="krumsiek11.h5ad"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
566 <conditional name="manipulate"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
567 <param name="function" value="flag_genes"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
568 <repeat name="gene_flags"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
569 <param name="startswith" value="Gata"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
570 <param name="col_name" value="Gata_TF"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
571 </repeat> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
572 <repeat name="gene_flags"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
573 <param name="startswith" value="Gf"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
574 <param name="col_name" value="GF"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
575 </repeat> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
12
diff
changeset
|
576 </conditional> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
577 <assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
578 <has_text_matching expression="500 × 11"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
579 </assert_stdout> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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580 <output name="anndata" ftype="h5ad"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
581 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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582 <has_h5_keys keys="var/Gata_TF"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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changeset
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583 <has_h5_keys keys="var/GF"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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584 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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changeset
|
585 </output> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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586 </test> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
587 <test expect_num_outputs="1"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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588 <!-- test 14 split_on_obs --> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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589 <param name="input" value="krumsiek11.h5ad"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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590 <conditional name="manipulate"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
591 <param name="function" value="split_on_obs"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
592 <param name="key" value="cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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593 </conditional> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
594 <output_collection name="output_h5ad_split" type="list"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
595 <element name="cell_type_0"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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596 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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597 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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598 <has_h5_keys keys="uns/highlights"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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599 <has_h5_keys keys="uns/iroot"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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600 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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changeset
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601 </element> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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changeset
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602 <element name="cell_type_1"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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diff
changeset
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603 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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changeset
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604 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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605 <has_h5_keys keys="uns/highlights"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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diff
changeset
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606 <has_h5_keys keys="uns/iroot"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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changeset
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607 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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changeset
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608 </element> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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changeset
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609 <element name="cell_type_2"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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diff
changeset
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610 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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611 <has_h5_keys keys="obs/cell_type"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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612 <has_h5_keys keys="uns/highlights"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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613 <has_h5_keys keys="uns/iroot"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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614 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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615 </element> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
|
616 <element name="cell_type_3"> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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617 <assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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618 <has_h5_keys keys="obs/cell_type"/> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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619 <has_h5_keys keys="uns/highlights"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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620 <has_h5_keys keys="uns/iroot"/> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents:
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diff
changeset
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621 </assert_contents> |
|
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
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622 </element> |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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623 </output_collection> |
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a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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624 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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625 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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626 <help><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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627 **What it does** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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628 |
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13
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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629 This tool takes a AnnData dataset, manipulates it and returns it. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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630 |
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13
7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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631 The possible manipulations are: |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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632 |
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9bd945a03d7b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
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633 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.concatenate.html>`__) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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634 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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635 The `uns`, `varm` and `obsm` attributes are ignored. |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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636 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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637 If you use `join='outer'` this fills 0s for sparse data when variables are absent in a batch. Use this with care. Dense data is filled with `NaN` |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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638 |
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9bd945a03d7b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
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639 - Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.obs_names_make_unique.html>`__) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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640 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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641 The first occurance of a non-unique value is ignored. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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642 |
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9bd945a03d7b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
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643 - Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.var_names_make_unique.html>`__) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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644 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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645 The first occurance of a non-unique value is ignored. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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646 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
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647 - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.rename_categories.html>`__) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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648 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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649 Besides calling `self.obs[key].cat.categories = categories` - similar for `var` - this also renames categories in unstructured annotation that uses the categorical annotation `key` |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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650 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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651 - Remove keys from obs or var annotations |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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652 |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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653 Helps in cleaning up andata with many annotations. For example, helps in removing qc metrics calculated during the preprocesing or already existing cluster annotations. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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654 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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655 - Flag genes start with a pattern |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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656 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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657 Useful for flagging the mitochoncdrial or ribosomal protein genes |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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658 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
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659 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.strings_to_categoricals.html>`__) |
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660 |
|
0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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661 Only affects string annotations that lead to less categories than the total number of observations. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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662 |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 58ea92c594280588f6045093d77af6d7d885185d"
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663 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.transpose.html>`__) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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664 |
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0ef28c0963c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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665 Data matrix is transposed, observations and variables are interchanged. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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666 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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667 - Add annotation for variables or |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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668 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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669 - Split the AnnData object into multiple AnnData objects based on the values of a given obs key |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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670 |
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7e8c677a7b71
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
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671 For example, helps in splitting an anndata objects based on cluster annotation. This function generates a collection with number of elements equal to the number of categories in the input obs key. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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672 |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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673 - Filter data variables or observations, by index or key |
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19592ec717ef
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 8ef5f7c6f8728608a3f05bb51e11b642b84a05f5"
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674 |
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a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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675 - Freeze the current state into the 'raw' attribute |
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a56baceb1900
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 3b41d687ff30583540d055f6995de00530cca81d"
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676 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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677 @HELP@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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678 ]]></help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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679 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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680 </tool> |