Mercurial > repos > iuc > modify_loom

annotate modify_loom.xml @ 10:db575b4c8b22 draft default tip

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 c1d84c1850c53deccc384de3960d2cec37bb2869
author iuc
date Fri, 08 Nov 2024 21:58:43 +0000
parents 0f1aaff9b22d
children
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>
10
db575b4c8b22 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit c1d84c1850c53deccc384de3960d2cec37bb2869
iuc
parents: 9
diff changeset
6 <expand macro="bio_tools"/>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
7 <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
8 <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
9 </expand>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
10 <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
11 <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
12 #if $operation.to_perform == 'manipulate'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
13 cp '${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
14 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
15 #if $operation.which_add.add_type == "cols":
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
16 -a cols -c '${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
17 #else if $operation.which_add.add_type == "rows":
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
18 -a rows -r '${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
19 #else if $operation.which_add.add_type == "layers":
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
20 -a layers -l '${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
21 #end if
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
22
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
23 #else if $operation.to_perform == 'export'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
24 mkdir ./output &&
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
25 mkdir ./attributes &&
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
26 python '$__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
27
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
28 #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
29 #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
30 @CMD@
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
31 #else if $operation.from.file_type == 'tab'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
32 python '$__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
33 -c '${operation.coldata}'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
34 -r '${operation.rowdata}'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
35 -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
36 #if $operation.other_files
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
37 '${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
38 #end if
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
39 #end if
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
40 #end if
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
41 ]]></command>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
42 <configfiles>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
43 <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
44 @CMD_imports@
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.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
46 #if $operation.from.file_type == 'ad'
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
47 adata = ad.read_h5ad('$operation.anndata')
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
48 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
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 #end if
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
51 ]]></configfile>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
52 </configfiles>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
53 <inputs>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
54 <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
55 <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
56 <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
57 <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
58 <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
59 </param>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
60 <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
61 <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
62 <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
63 <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
64 <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
65 <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
66 <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
67 </param>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
68 <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
69 <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
70 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
71 <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
72 <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
73 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
74 <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
75 <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
76 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
77 </conditional>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
78 </when>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
79 <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
80 <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
81 </when>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
82 <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
83 <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
84 <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
85 <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
86 <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
87 </param>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
88 <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
89 <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
90 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
91 <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
92 <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
93 <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
94 <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
95 <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
96 </when>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
97 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
98
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
99 </when>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
100 </conditional>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
101 </inputs>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
102 <outputs>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
103 <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
104 <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
105 </data>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
106 <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
107 <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
108 <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
109 </collection>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
110 <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
111 <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
112 <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
113 </collection>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
114 </outputs>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
115 <tests>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
116 <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
117 <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
118 <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
119 <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
120 <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
121 <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
122 <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
123 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
124 </conditional>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
125 <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
126 </test>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
127 <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
128 <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
129 <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
130 <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
131 <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
132 <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
133 <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
134 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
135 </conditional>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
136 <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
137 </test>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
138 <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
139 <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
140 <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
141 <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
142 <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
143 <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
144 <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
145 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
146 </conditional>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
147 <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
148 </test>
9
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
149 <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
150 <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
151 <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
152 <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
153 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
154 <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
155 <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
156 <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
157 <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
158 </output_collection>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
159 <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
160 <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
161 <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
162 </output_collection>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
163 </test>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
164 <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
165 <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
166 <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
167 <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
168 <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
169 <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
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 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
172 <assert_stdout>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
173 <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
174 </assert_stdout>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
175 <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
176 </test>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
177 <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
178 <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
179 <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
180 <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
181 <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
182 <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
183 <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
184 <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
185 <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
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 </conditional>
0f1aaff9b22d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit 67b3808b56df343798263ff0c905df8cb789edfa
iuc
parents: 7
diff changeset
188 <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
189 </test>
0
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
190 </tests>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
191 <help><![CDATA[
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
192 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
193 ]]></help>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
194 <citations>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
195 <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
196 author = "Linnarsson lab"
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
197 title = "Loompy"
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
198 year = "2013"
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
199 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
200 </citation>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
201 </citations>
c8e4d0b9ae8c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
iuc
parents:
diff changeset
202 </tool>