Mercurial > repos > iuc > modify_loom

annotate modify_loom.xml @ 9:0f1aaff9b22d draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
author iuc
date Sat, 14 Sep 2024 19:59:12 +0000
parents 4b0adaa31c95
children db575b4c8b22
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
1 <tool id="modify_loom" name="Loom operations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
2 <description>Manipulate, export and import loom data</description>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
3 <macros>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
4 <import>macros.xml</import>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
5 </macros>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
6 <expand macro="requirements">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
7 <requirement type="package" version="1.26.4">numpy</requirement><!-- loompy seems to adapt to numpy 2.x. Remove this in the next update -->
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
8 </expand>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
9 <expand macro="version_command"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
11 #if $operation.to_perform == 'manipulate'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
12 cp '${operation.loom}' converted.loom &&
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
13 python '$__tool_directory__/modify_loom.py' -f 'converted.loom'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
14 #if $operation.which_add.add_type == "cols":
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
15 -a cols -c '${operation.which_add.cols}'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
16 #else if $operation.which_add.add_type == "rows":
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
17 -a rows -r '${operation.which_add.rows}'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
18 #else if $operation.which_add.add_type == "layers":
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
19 -a layers -l '${operation.which_add.layers}'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
20 #end if
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
21
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
22 #else if $operation.to_perform == 'export'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
23 mkdir ./output &&
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
24 mkdir ./attributes &&
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
25 python '$__tool_directory__/loompy_to_tsv.py' -f '$operation.loom'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
26
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
27 #else if $operation.to_perform == 'import'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
28 #if $operation.from.file_type == 'ad'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
29 @CMD@
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
30 #else if $operation.from.file_type == 'tab'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
31 python '$__tool_directory__/tsv_to_loompy.py'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
32 -c '${operation.coldata}'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
33 -r '${operation.rowdata}'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
34 -f '${operation.mainmatrix}'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
35 #if $operation.other_files
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
36 '${operation.other_files}'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
37 #end if
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
38 #end if
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
39 #end if
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
40 ]]></command>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
41 <configfiles>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
42 <configfile name="script_file"><![CDATA[
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
43 @CMD_imports@
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
44 #if $operation.to_perform == 'import'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
45 #if $operation.from.file_type == 'ad'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
46 adata = ad.read_h5ad('$operation.anndata')
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
47 adata.write_loom('converted.loom')
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
48 #end if
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
49 #end if
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
50 ]]></configfile>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
51 </configfiles>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
52 <inputs>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
53 <conditional name="operation">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
54 <param name="to_perform" type="select" label="Operation to perform on loom data">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
55 <option value="manipulate">Manipulate loom data</option>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
56 <option value="export">Export loom layers and attributes</option>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
57 <option value="import">Import loom from an anndata or tabular files</option>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
58 </param>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
59 <when value="manipulate">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
60 <param name="loom" type="data" format="loom" label="Loom file"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
61 <conditional name="which_add">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
62 <param name="add_type" type="select" label="Select data attribute to add to loom">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
63 <option value="cols">Columns</option>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
64 <option value="rows">Rows</option>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
65 <option value="layers">Layers</option>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
66 </param>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
67 <when value="cols">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
68 <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
69 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
70 <when value="rows">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
71 <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
72 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
73 <when value="layers">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
74 <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
75 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
76 </conditional>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
77 </when>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
78 <when value="export">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
79 <param name="loom" type="data" format="loom" label="Loom file"/>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
80 </when>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
81 <when value="import">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
82 <conditional name="from">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
83 <param name="file_type" type="select" label="Create loom file from">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
84 <option value="ad">an anndata object</option>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
85 <option value="tab">from tabular files of matrix and row and column attributes</option>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
86 </param>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
87 <when value="ad">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
88 <param name="anndata" type="data" format="h5ad" label="Anndata file"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
89 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
90 <when value="tab">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
91 <param name="mainmatrix" type="data" format="tabular" label="File for main layer of loom file." help="All subsequent tsv must be the same dimensions as this file. When converted back to tsv using hd5 export, this will be labeled as 'mainmatrix.tsv'"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
92 <param name="other_files" type="data" format="tabular" multiple="true" optional="true" label="Add layers" help="Adds layers of same dimension to the loom file. When converted to tsv using hd5 export, these layers will retain their names."/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
93 <param name="coldata" type="data" format="tabular" label="Tsv of column data." help="First row is column attributes, subsequent are values."/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
94 <param name="rowdata" type="data" format="tabular" label="Tsv of row data." help="First row is row attributes, subsequent are values."/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
95 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
96 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
97
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
98 </when>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
99 </conditional>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
100 </inputs>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
101 <outputs>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
102 <data name="loomout" format="loom" from_work_dir='converted.loom' label="${tool.name} (${operation.to_perform}) on ${on_string} Loom file">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
103 <filter>operation['to_perform'] == 'manipulate' or operation['to_perform'] == 'import'</filter>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
104 </data>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
105 <collection name="layer_tsvs" type="list" label="Layer matrices" >
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
106 <filter>operation['to_perform'] == 'export'</filter>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
107 <discover_datasets pattern="__designation__" format="tabular" directory="output" visible="false" />
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
108 </collection>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
109 <collection name="attribute_tsvs" type="list" label="Attribute matrices" >
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
110 <filter>operation['to_perform'] == 'export'</filter>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
111 <discover_datasets pattern="__designation__" format="tabular" directory="attributes" visible="false" />
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
112 </collection>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
113 </outputs>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
114 <tests>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
115 <test expect_num_outputs="1">
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
116 <conditional name="operation">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
117 <param name="to_perform" value="manipulate"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
118 <param name="loom" value="addtest.loom"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
119 <conditional name="which_add">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
120 <param name="add_type" value="cols"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
121 <param name="cols" value="cols.tsv"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
122 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
123 </conditional>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
124 <output name="loomout" value="addloomout1.loom" ftype="loom" compare="sim_size"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
125 </test>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
126 <test expect_num_outputs="1">
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
127 <conditional name="operation">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
128 <param name="to_perform" value="manipulate"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
129 <param name="loom" value="addtest.loom"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
130 <conditional name="which_add">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
131 <param name="add_type" value="rows"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
132 <param name="rows" value="rows.tsv"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
133 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
134 </conditional>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
135 <output name="loomout" value="addloomout2.loom" ftype="loom" compare="sim_size"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
136 </test>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
137 <test expect_num_outputs="1">
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
138 <conditional name="operation">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
139 <param name="to_perform" value="manipulate"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
140 <param name="loom" value="addtest.loom"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
141 <conditional name="which_add">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
142 <param name="add_type" value="layers"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
143 <param name="layers" value="addlayer1.tsv"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
144 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
145 </conditional>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
146 <output name="loomout" value="addloomout3.loom" ftype="loom" compare="sim_size"/>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
147 </test>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
148 <test expect_num_outputs="2">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
149 <conditional name="operation">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
150 <param name="to_perform" value="export"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
151 <param name="loom" value="loomtest.loom"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
152 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
153 <output_collection name="layer_tsvs" type="list">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
154 <element name="extralayer.tsv" value="secondlayer.tsv" ftype="tabular"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
155 <element name="mainmatrix.tsv" value="firstlayer.tsv" ftype="tabular"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
156 <element name="thirdlayer.tsv" value="finallayer.tsv" ftype="tabular"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
157 </output_collection>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
158 <output_collection name="attribute_tsvs" type="list">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
159 <element name="col_attr.tsv" value="cols.tsv" ftype="tabular"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
160 <element name="row_attr.tsv" value="rows.tsv" ftype="tabular"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
161 </output_collection>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
162 </test>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
163 <test expect_num_outputs="1">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
164 <conditional name="operation">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
165 <param name="to_perform" value="import"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
166 <conditional name="from">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
167 <param name="file_type" value="ad"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
168 <param name="anndata" value="krumsiek11.h5ad"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
169 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
170 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
171 <assert_stdout>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
172 <has_text_matching expression="adata.write_loom"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
173 </assert_stdout>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
174 <output name="loomout" value="export.krumsiek11.loom" ftype="loom" compare="sim_size"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
175 </test>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
176 <test expect_num_outputs="1">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
177 <conditional name="operation">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
178 <param name="to_perform" value="import"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
179 <conditional name="from">
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
180 <param name="file_type" value="tab"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
181 <param name="mainmatrix" value="firstlayer.tsv"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
182 <param name="other_files" value="secondlayer.tsv"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
183 <param name="coldata" value="cols.tsv"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
184 <param name="rowdata" value="rows.tsv"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
185 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
186 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
187 <output name="loomout" value="converted.loom.test" ftype="loom" compare="sim_size"/>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
188 </test>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
189 </tests>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
190 <help><![CDATA[
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
191 This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
192 ]]></help>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
193 <citations>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
194 <citation type="bibtex">@UNPUBLISHED{Linnarsson2016,
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
195 author = "Linnarsson lab"
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
196 title = "Loompy"
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
197 year = "2013"
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
198 note = "https://github.com/linnarsson-lab/loompy"}
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
199 </citation>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
200 </citations>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
201 </tool>