Mercurial > repos > iuc > anndata_manipulate

annotate manipulate.xml @ 0:0ef28c0963c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
author iuc
date Wed, 10 Apr 2019 03:25:05 -0400
parents
children 19592ec717ef
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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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1 <tool id="anndata_manipulate" name="Manipulate AnnData" version="@VERSION@+@GALAXY_VERSION@">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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2 <description>object</description>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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3 <macros>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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4 <import>macros.xml</import>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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5 <xml name="param_join">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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6 <param name="join" type="select" label="The connecting string between name and integer">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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7 <option value="-">-</option>
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8 <option value="_">_</option>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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9 <option value=" "> </option>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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10 <option value="/">/</option>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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11 </param>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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12 </xml>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
iuc
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13 </macros>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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14 <expand macro="requirements"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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15 <expand macro="version_command"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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16 <command detect_errors="exit_code"><![CDATA[
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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17 @CMD@
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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18 ]]></command>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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19 <configfiles>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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20 <configfile name="script_file"><![CDATA[
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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21 @CMD_imports@
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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22
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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23 adata = ad.read('$input')
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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24
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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25 #if $manipulate.function == 'concatenate'
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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26 #for i, filepath in enumerate($manipulate.other_adatas)
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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27 adata_$i = ad.read('$filepath')
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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28 #end for
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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29 adata.concatenate(
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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30 #for i, filepath in enumerate($manipulate.other_adatas)
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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31 adata_$i,
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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32 #end for
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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33 join='$manipulate.join',
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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34 #if str($manipulate.index_unique) != ''
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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35 index_unique='$manipulate.index_unique',
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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36 #else
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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37 index_unique=None,
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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38 #end if
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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39 batch_key='$manipulate.batch_key')
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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40
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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41 #else if $manipulate.function == 'var_names_make_unique'
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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42 adata.var_names_make_unique(join='$manipulate.join')
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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43
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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44 #else if $manipulate.function == 'obs_names_make_unique'
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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45 adata.obs_names_make_unique(join='$manipulate.join')
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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46
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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47 #else if $manipulate.function == 'rename_categories'
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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48 #set $categories = [x.strip() for x in str($manipulate.categories).split(',')]
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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49 adata.rename_categories(
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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50 key='$manipulate.key',
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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51 categories=$categories)
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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52
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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53 #else if $manipulate.function == 'transpose'
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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54 adata.transpose()
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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55
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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56 #else if $manipulate.function == 'strings_to_categoricals'
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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57 adata.strings_to_categoricals()
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58 #end if
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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59
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60 adata.write('anndata.h5ad')
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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61 ]]></configfile>
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62 </configfiles>
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63 <inputs>
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64 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
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65 <conditional name="manipulate">
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66 <param name="function" type="select" label="Function of manipulate the object">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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67 <option value="concatenate">Concatenate along the observations axis</option>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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68 <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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69 <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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70 <option value="rename_categories">Rename categories of annotation</option>
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71 <option value="strings_to_categoricals">Transform string annotations to categoricals</option>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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72 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>
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73 </param>
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74 <when value="concatenate">
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75 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
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76 <param name="join" type="select" label="Join method">
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77 <option value="inner">Intersection of variables</option>
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78 <option value="outer">Union of variables</option>
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79 </param>
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80 <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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81 <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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82 <option value="-">-</option>
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83 <option value="_">_</option>
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84 <option value=" "> </option>
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85 <option value="/">/</option>
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86 </param>
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87 </when>
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88 <when value="obs_names_make_unique">
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89 <expand macro="param_join"/>
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90 </when>
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91 <when value="var_names_make_unique">
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92 <expand macro="param_join"/>
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93 </when>
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94 <when value="rename_categories">
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95 <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/>
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96 <param name="categories" type="text" value="" label="Comma-separated list of new categories" help="It should be the same number as the old categories"/>
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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97 </when>
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98 <when value="strings_to_categoricals"/>
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99 <when value="transpose"/>
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100 </conditional>
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101 </inputs>
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102 <outputs>
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103 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}"/>
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104 </outputs>
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105 <tests>
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106 <test>
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107 <param name="input" value="krumsiek11.h5ad"/>
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108 <conditional name="manipulate">
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109 <param name="function" value="concatenate"/>
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110 <param name="other_adatas" value="import.csv.h5ad"/>
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111 <param name="join" value="inner"/>
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112 <param name="batch_key" value="batch"/>
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113 <param name="index_unique" value="-"/>
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114 </conditional>
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115 <assert_stdout>
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116 <has_text_matching expression="adata_0"/>
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117 <has_text_matching expression="adata.concatenate"/>
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118 <has_text_matching expression="join='inner'"/>
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119 <has_text_matching expression="index_unique='-'"/>
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120 <has_text_matching expression="batch_key='batch'"/>
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121 </assert_stdout>
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122 <output name="anndata" value="manipulate.concatenate.h5ad" ftype="h5ad" compare="sim_size"/>
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123 </test>
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124 <test>
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125 <param name="input" value="krumsiek11.h5ad"/>
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126 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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127 <param name="function" value="obs_names_make_unique"/>
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128 <param name="join" value="-"/>
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129 </conditional>
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130 <assert_stdout>
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131 <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/>
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132 </assert_stdout>
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133 <output name="anndata" value="manipulate.obs_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
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134 </test>
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135 <test>
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136 <param name="input" value="krumsiek11.h5ad"/>
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137 <conditional name="manipulate">
0ef28c0963c8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 2e16aca90c4fc6f13bd024eed43bc4adbf5967da
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138 <param name="function" value="var_names_make_unique"/>
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139 <param name="join" value="-"/>
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140 </conditional>
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141 <assert_stdout>
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142 <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/>
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143 </assert_stdout>
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144 <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
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145 </test>
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146 <test>
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147 <param name="input" value="krumsiek11.h5ad"/>
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148 <conditional name="manipulate">
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149 <param name="function" value="rename_categories"/>
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150 <param name="key" value="cell_type"/>
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151 <param name="categories" value="Er,Ml,Mt, Ne, pr"/>
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152 </conditional>
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153 <assert_stdout>
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154 <has_text_matching expression="adata.rename_categories"/>
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155 <has_text_matching expression="key='cell_type'"/>
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156 <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/>
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157 </assert_stdout>
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158 <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>
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159 </test>
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160 <test>
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161 <param name="input" value="krumsiek11.h5ad"/>
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162 <conditional name="manipulate">
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163 <param name="function" value="strings_to_categoricals"/>
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164 </conditional>
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165 <assert_stdout>
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166 <has_text_matching expression="adata.strings_to_categoricals"/>
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167 </assert_stdout>
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168 <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/>
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169 </test>
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170 <test>
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171 <param name="input" value="krumsiek11.h5ad"/>
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172 <conditional name="manipulate">
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173 <param name="function" value="transpose"/>
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174 </conditional>
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175 <assert_stdout>
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176 <has_text_matching expression="adata.transpose"/>
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177 </assert_stdout>
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178 <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/>
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179 </test>
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180 </tests>
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181 <help><![CDATA[
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182 **What it does**
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183
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184 This tool takes a AnnData dataset, manipulates it and returns it.
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185
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186 The possible manipulations are:
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187
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188 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.concatenate.html>`__)
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189
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190 The `uns`, `varm` and `obsm` attributes are ignored.
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191
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192 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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193
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194 - Makes the obs index unique by appending '1', '2', etc (`obs_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.obs_names_make_unique.html>`__)
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195
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196 The first occurance of a non-unique value is ignored.
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197
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198 - Makes the var index unique by appending '1', '2', etc (`var_names_make_unique method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.var_names_make_unique.html>`__)
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199
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200 The first occurance of a non-unique value is ignored.
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201
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202 - Rename categories of annotation `key` in `obs`, `var` and `uns` (`rename_categories method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.rename_categories.html>`__)
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203
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204 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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205
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206 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.strings_to_categoricals.html>`__)
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207
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208 Only affects string annotations that lead to less categories than the total number of observations.
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209
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210 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__)
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211
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212 Data matrix is transposed, observations and variables are interchanged.
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213
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214 @HELP@
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215 ]]></help>
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216 <expand macro="citations"/>
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217 </tool>