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comparison export.xml @ 11:2411ca833c18 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
author iuc
date Sat, 14 Sep 2024 19:55:32 +0000
parents 87254cd3a609
children 155982133d99
comparison
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10:87254cd3a609 11:2411ca833c18
1 <tool id="anndata_export" name="Export AnnData and loom files" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 1 <tool id="anndata_export" name="Export AnnData" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Interconvert AnnData and Loom formats</description> 2 <description>matrix and annotations</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="version_command"/> 7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9 #if $hd5_format.filetype == 'anndata': 9 @CMD@
10 @CMD@
11 #else:
12 @LOOMCMD@
13 #end if
14 ]]></command> 10 ]]></command>
15 <configfiles> 11 <configfiles>
16 <configfile name="script_file"><![CDATA[ 12 <configfile name="script_file"><![CDATA[
17 @CMD_imports@ 13 @CMD_imports@
18 #if $hd5_format.filetype == 'anndata': 14 adata = ad.read_h5ad('$input')
19 adata = ad.read('$hd5_format.input')
20 #if $hd5_format.output_format == 'loom':
21 adata.write_loom('anndata.loom')
22 #else if $hd5_format.output_format == 'tabular':
23 adata.write_csvs('.', sep="\t", skip_data = False) 15 adata.write_csvs('.', sep="\t", skip_data = False)
24 #end if
25 #end if
26 ]]></configfile> 16 ]]></configfile>
27 </configfiles> 17 </configfiles>
28 <inputs> 18 <inputs>
29 <conditional name="hd5_format"> 19 <param name="input" type="data" format="h5ad" label="Annotated data matrix to export" help="Create individual tabular files for matrix, obs, obsm, var and varm annotations"/>
30 <param name="filetype" type="select" label="hd5 format">
31 <option value="anndata" selected="true">Anndata file</option>
32 <option value="loom">Loom file</option>
33 </param>
34 <when value="anndata">
35 <param name="input" type="data" format="h5ad" label="Annotated data matrix"/>
36 <param name="output_format" type="select" label="Format to write the annotated data matrix">
37 <option value="loom">loom</option>
38 <option value="tabular">Tabular</option>
39 </param>
40 </when>
41 <when value="loom">
42 <param name="input" type="data" format="loom" label="Loom file to be exported to a series of tabular files."/>
43 </when>
44 </conditional>
45 </inputs> 20 </inputs>
46 <outputs> 21 <outputs>
47 <data name="loom_output" format="loom" from_work_dir="anndata.loom" label="${tool.name} on ${on_string}: Annotated data matrix"> 22 <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)"/>
48 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'loom'</filter> 23 <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)"/>
49 </data> 24 <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)"/>
50 <data name="tabular_x" format="tabular" from_work_dir="X.csv" label="${tool.name} on ${on_string}: Matrix table (X)"> 25 <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)"/>
51 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter> 26 <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)"/>
52 </data>
53 <data name="tabular_obs" format="tabular" from_work_dir="obs.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional observations annotation (obs)">
54 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
55 </data>
56 <data name="tabular_obsm" format="tabular" from_work_dir="obsm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional observations annotation (obsm)">
57 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
58 </data>
59 <data name="tabular_var" format="tabular" from_work_dir="var.csv" label="${tool.name} on ${on_string}: Key-indexed one-dimensional variables annotation (var)">
60 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
61 </data>
62 <data name="tabular_varm" format="tabular" from_work_dir="varm.csv" label="${tool.name} on ${on_string}: Key-indexed multi-dimensional variables annotation (varm)">
63 <filter>hd5_format['filetype'] == 'anndata' and hd5_format['output_format'] == 'tabular'</filter>
64 </data>
65 <collection name="layer_tsvs" type="list" label="Layer matrices" >
66 <filter>hd5_format['filetype'] == 'loom'</filter>
67 <discover_datasets pattern="__designation__" format="tabular" directory="output" visible="false" />
68 </collection>
69 <collection name="attribute_tsvs" type="list" label="Attribute matrices" >
70 <filter>hd5_format['filetype'] == 'loom'</filter>
71 <discover_datasets pattern="__designation__" format="tabular" directory="attributes" visible="false" />
72 </collection>
73 </outputs> 27 </outputs>
74 <tests> 28 <tests>
75 <test expect_num_outputs="1"> 29 <test expect_num_outputs="5">
76 <param name="filetype" value="anndata"/>
77 <param name="input" value="krumsiek11.h5ad"/> 30 <param name="input" value="krumsiek11.h5ad"/>
78 <param name="output_format" value="loom"/>
79 <assert_stdout>
80 <has_text_matching expression="adata.write_loom"/>
81 </assert_stdout>
82 <output name="loom_output" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
83 </test>
84 <test expect_num_outputs="5">
85 <param name="filetype" value="anndata"/>
86 <param name="input" value="krumsiek11.h5ad"/>
87 <param name="output_format" value="tabular"/>
88 <assert_stdout> 31 <assert_stdout>
89 <has_text_matching expression="adata.write_csvs"/> 32 <has_text_matching expression="adata.write_csvs"/>
90 </assert_stdout> 33 </assert_stdout>
91 <output name="tabular_x" value="export.krumsiek11.X.tabular" ftype="tabular"/> 34 <output name="tabular_x" value="export.krumsiek11.X.tabular" ftype="tabular"/>
92 <output name="tabular_obs" value="export.krumsiek11.obs.tabular" ftype="tabular"/> 35 <output name="tabular_obs" value="export.krumsiek11.obs.tabular" ftype="tabular"/>
93 <output name="tabular_obsm" value="export.krumsiek11.obsm.tabular" ftype="tabular"/> 36 <output name="tabular_obsm" value="export.krumsiek11.obsm.tabular" ftype="tabular"/>
94 <output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/> 37 <output name="tabular_var" value="export.krumsiek11.var.tabular" ftype="tabular"/>
95 <output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/> 38 <output name="tabular_varm" value="export.krumsiek11.varm.tabular" ftype="tabular"/>
96 </test> 39 </test>
97 <test expect_num_outputs="2">
98 <param name="filetype" value="loom"/>
99 <param name="input" value="loomtest.loom"/>
100 <output_collection name="layer_tsvs" type="list">
101 <element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/>
102 <element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/>
103 <element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/>
104 </output_collection>
105 <output_collection name="attribute_tsvs" type="list">
106 <element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/>
107 <element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/>
108 </output_collection>
109 </test>
110 </tests> 40 </tests>
111 <help><![CDATA[ 41 <help><![CDATA[
112 This tool exports an AnnData dataset to a Loom file 42 This tool exports an AnnData dataset to a tabular files (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)
113 (`write_loom method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_loom.html>`__)
114 or a Tabular file (`write_csvs method <https://anndata.readthedocs.io/en/latest/generated/anndata.AnnData.write_csvs.html>`__)
115
116 It can also create a series of tabular files from an input loom dataset.
117 43
118 @HELP@ 44 @HELP@
119 ]]></help> 45 ]]></help>
120 <expand macro="citations"/> 46 <expand macro="citations"/>
121 </tool> 47 </tool>