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comparison 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
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children 19592ec717ef
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-1:000000000000 0:0ef28c0963c8
1 <tool id="anndata_manipulate" name="Manipulate AnnData" version="@VERSION@+@GALAXY_VERSION@">
2 <description>object</description>
3 <macros>
4 <import>macros.xml</import>
5 <xml name="param_join">
6 <param name="join" type="select" label="The connecting string between name and integer">
7 <option value="-">-</option>
8 <option value="_">_</option>
9 <option value=" "> </option>
10 <option value="/">/</option>
11 </param>
12 </xml>
13 </macros>
14 <expand macro="requirements"/>
15 <expand macro="version_command"/>
16 <command detect_errors="exit_code"><![CDATA[
17 @CMD@
18 ]]></command>
19 <configfiles>
20 <configfile name="script_file"><![CDATA[
21 @CMD_imports@
22
23 adata = ad.read('$input')
24
25 #if $manipulate.function == 'concatenate'
26 #for i, filepath in enumerate($manipulate.other_adatas)
27 adata_$i = ad.read('$filepath')
28 #end for
29 adata.concatenate(
30 #for i, filepath in enumerate($manipulate.other_adatas)
31 adata_$i,
32 #end for
33 join='$manipulate.join',
34 #if str($manipulate.index_unique) != ''
35 index_unique='$manipulate.index_unique',
36 #else
37 index_unique=None,
38 #end if
39 batch_key='$manipulate.batch_key')
40
41 #else if $manipulate.function == 'var_names_make_unique'
42 adata.var_names_make_unique(join='$manipulate.join')
43
44 #else if $manipulate.function == 'obs_names_make_unique'
45 adata.obs_names_make_unique(join='$manipulate.join')
46
47 #else if $manipulate.function == 'rename_categories'
48 #set $categories = [x.strip() for x in str($manipulate.categories).split(',')]
49 adata.rename_categories(
50 key='$manipulate.key',
51 categories=$categories)
52
53 #else if $manipulate.function == 'transpose'
54 adata.transpose()
55
56 #else if $manipulate.function == 'strings_to_categoricals'
57 adata.strings_to_categoricals()
58 #end if
59
60 adata.write('anndata.h5ad')
61 ]]></configfile>
62 </configfiles>
63 <inputs>
64 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
65 <conditional name="manipulate">
66 <param name="function" type="select" label="Function of manipulate the object">
67 <option value="concatenate">Concatenate along the observations axis</option>
68 <option value="obs_names_make_unique">Makes the obs index unique by appending '1', '2', etc</option>
69 <option value="var_names_make_unique">Makes the var index unique by appending '1', '2', etc</option>
70 <option value="rename_categories">Rename categories of annotation</option>
71 <option value="strings_to_categoricals">Transform string annotations to categoricals</option>
72 <option value="transpose">Transpose the data matrix, leaving observations and variables interchanged</option>
73 </param>
74 <when value="concatenate">
75 <param name="other_adatas" type="data" format="h5ad" multiple="true" label="Annotated data matrix to add"/>
76 <param name="join" type="select" label="Join method">
77 <option value="inner">Intersection of variables</option>
78 <option value="outer">Union of variables</option>
79 </param>
80 <param name="batch_key" type="text" value="batch" label="Key to add the batch annotation to obs"/>
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">
82 <option value="-">-</option>
83 <option value="_">_</option>
84 <option value=" "> </option>
85 <option value="/">/</option>
86 </param>
87 </when>
88 <when value="obs_names_make_unique">
89 <expand macro="param_join"/>
90 </when>
91 <when value="var_names_make_unique">
92 <expand macro="param_join"/>
93 </when>
94 <when value="rename_categories">
95 <param name="key" type="text" value="" label="Key for observations or variables annotation" help="Annotation key in obs or var"/>
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"/>
97 </when>
98 <when value="strings_to_categoricals"/>
99 <when value="transpose"/>
100 </conditional>
101 </inputs>
102 <outputs>
103 <data name="anndata" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}"/>
104 </outputs>
105 <tests>
106 <test>
107 <param name="input" value="krumsiek11.h5ad"/>
108 <conditional name="manipulate">
109 <param name="function" value="concatenate"/>
110 <param name="other_adatas" value="import.csv.h5ad"/>
111 <param name="join" value="inner"/>
112 <param name="batch_key" value="batch"/>
113 <param name="index_unique" value="-"/>
114 </conditional>
115 <assert_stdout>
116 <has_text_matching expression="adata_0"/>
117 <has_text_matching expression="adata.concatenate"/>
118 <has_text_matching expression="join='inner'"/>
119 <has_text_matching expression="index_unique='-'"/>
120 <has_text_matching expression="batch_key='batch'"/>
121 </assert_stdout>
122 <output name="anndata" value="manipulate.concatenate.h5ad" ftype="h5ad" compare="sim_size"/>
123 </test>
124 <test>
125 <param name="input" value="krumsiek11.h5ad"/>
126 <conditional name="manipulate">
127 <param name="function" value="obs_names_make_unique"/>
128 <param name="join" value="-"/>
129 </conditional>
130 <assert_stdout>
131 <has_text_matching expression="adata.obs_names_make_unique\(join='-'\)"/>
132 </assert_stdout>
133 <output name="anndata" value="manipulate.obs_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
134 </test>
135 <test>
136 <param name="input" value="krumsiek11.h5ad"/>
137 <conditional name="manipulate">
138 <param name="function" value="var_names_make_unique"/>
139 <param name="join" value="-"/>
140 </conditional>
141 <assert_stdout>
142 <has_text_matching expression="adata.var_names_make_unique\(join='-'\)"/>
143 </assert_stdout>
144 <output name="anndata" value="manipulate.var_names_make_unique.h5ad" ftype="h5ad" compare="sim_size"/>
145 </test>
146 <test>
147 <param name="input" value="krumsiek11.h5ad"/>
148 <conditional name="manipulate">
149 <param name="function" value="rename_categories"/>
150 <param name="key" value="cell_type"/>
151 <param name="categories" value="Er,Ml,Mt, Ne, pr"/>
152 </conditional>
153 <assert_stdout>
154 <has_text_matching expression="adata.rename_categories"/>
155 <has_text_matching expression="key='cell_type'"/>
156 <has_text_matching expression="categories=\['Er', 'Ml', 'Mt', 'Ne', 'pr'\]"/>
157 </assert_stdout>
158 <output name="anndata" value="manipulate.rename_categories.h5ad" ftype="h5ad" compare="sim_size"/>
159 </test>
160 <test>
161 <param name="input" value="krumsiek11.h5ad"/>
162 <conditional name="manipulate">
163 <param name="function" value="strings_to_categoricals"/>
164 </conditional>
165 <assert_stdout>
166 <has_text_matching expression="adata.strings_to_categoricals"/>
167 </assert_stdout>
168 <output name="anndata" value="manipulate.strings_to_categoricals.h5ad" ftype="h5ad" compare="sim_size"/>
169 </test>
170 <test>
171 <param name="input" value="krumsiek11.h5ad"/>
172 <conditional name="manipulate">
173 <param name="function" value="transpose"/>
174 </conditional>
175 <assert_stdout>
176 <has_text_matching expression="adata.transpose"/>
177 </assert_stdout>
178 <output name="anndata" value="manipulate.transpose.h5ad" ftype="h5ad" compare="sim_size"/>
179 </test>
180 </tests>
181 <help><![CDATA[
182 **What it does**
183
184 This tool takes a AnnData dataset, manipulates it and returns it.
185
186 The possible manipulations are:
187
188 - Concatenate along the observations axis (`concatenate method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.concatenate.html>`__)
189
190 The `uns`, `varm` and `obsm` attributes are ignored.
191
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`
193
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>`__)
195
196 The first occurance of a non-unique value is ignored.
197
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>`__)
199
200 The first occurance of a non-unique value is ignored.
201
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>`__)
203
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`
205
206 - Transform string annotations to categoricals (`strings_to_categoricals method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.strings_to_categoricals.html>`__)
207
208 Only affects string annotations that lead to less categories than the total number of observations.
209
210 - Transpose the data matrix, leaving observations and variables interchanged (`transpose method <https://anndata.readthedocs.io/en/latest/anndata.AnnData.transpose.html>`__)
211
212 Data matrix is transposed, observations and variables are interchanged.
213
214 @HELP@
215 ]]></help>
216 <expand macro="citations"/>
217 </tool>