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comparison modify_loom.xml @ 0:c8e4d0b9ae8c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/anndata/ commit dc9d19d1f902f3ed54009cd0e68c8518c284b856"
author iuc
date Mon, 06 Jan 2020 13:43:38 -0500
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-1:000000000000 0:c8e4d0b9ae8c
1 <tool id="modify_loom" name="Manipulate loom object" version="@VERSION@+@GALAXY_VERSION@">
2 <description>Add layers, or row/column attributes to a loom file</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="exit_code"><![CDATA[
9 python '$__tool_directory__/modify_loom.py' -f '${input}'
10 #if $which_add.add_type == "cols":
11 -a cols -c '${which_add.cols}'
12 #else if $which_add.add_type == "cols":
13 -a rows -r '${which_add.rows}'
14 #else if $which_add.add_type == "layers":
15 -a layers -l '${which_add.layers}'
16 #end if
17 && cp '${input}' loom_add_out.loom
18 ]]></command>
19 <inputs>
20 <param name="input" type="data" format="loom" label="Loom file"/>
21 <conditional name="which_add">
22 <param name="add_type" type="select" label="Select data attribute to add to loom">
23 <option value="cols">Columns</option>
24 <option value="rows">Rows</option>
25 <option value="layers">Layers</option>
26 </param>
27 <when value="cols">
28 <param name="cols" type="data" format="tabular" label="Column file of same dimensions as existing file"/>
29 </when>
30 <when value="rows">
31 <param name="rows" type="data" format="tabular" label="Row file of same dimensions as existing file"/>
32 </when>
33 <when value="layers">
34 <param name="layers" type="data" multiple="true" format="tabular" label="Layer file(s) of same dimensions as existing file"/>
35 </when>
36 </conditional>
37 </inputs>
38 <outputs>
39 <data name="loomout" format="loom" from_work_dir='loom_add_out.loom' label="Expanded loom file from '${on_string}'"/>
40 </outputs>
41 <tests>
42 <test expect_num_outputs="1">
43 <param name="input" value="addtest.loom"/>
44 <param name="add_type" value="cols"/>
45 <param name="cols" value="cols.tsv"/>
46 <output name="loomout" value="addloomout1.loom" ftype="loom" compare="sim_size"/>
47 </test>
48 <test expect_num_outputs="1">
49 <param name="input" value="addtest.loom"/>
50 <param name="add_type" value="rows"/>
51 <param name="rows" value="rows.tsv"/>
52 <output name="loomout" value="addloomout2.loom" ftype="loom" compare="sim_size"/>
53 </test>
54 <test expect_num_outputs="1">
55 <param name="input" value="addtest.loom"/>
56 <param name="add_type" value="layers"/>
57 <param name="layers" value="addlayer1.tsv"/>
58 <output name="loomout" value="addloomout3.loom" ftype="loom" compare="sim_size"/>
59 </test>
60 </tests>
61 <help><![CDATA[
62 This tool allows the user to modify an existing loom data file by adding column attributes, row attributes or additional layers via tsv files.
63 ]]></help>
64 <citations>
65 <citation type="bibtex">@UNPUBLISHED{Linnarsson2016,
66 author = "Linnarsson lab"
67 title = "Loompy"
68 year = "2013"
69 note = "https://github.com/linnarsson-lab/loompy"}
70 </citation>
71 </citations>
72 </tool>