Mercurial > repos > goeckslab > scimap_anndata_to_csv

comparison anndata_to_csv.xml @ 0:199b5f278356 draft

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planemo upload for repository https://github.com/goeckslab/tools-mti/tree/main/tools/scimap commit 9fb5578191db8a559191e45156cfb95350f01aea
author goeckslab
date Mon, 10 Jun 2024 18:44:49 +0000
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1 <tool id="scimap_anndata_to_csv" name="Convert Anndata to CSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>with Scimap</description>
3 <macros>
4 <import>main_macros.xml</import>
5 </macros>
6 <expand macro="scimap_requirements" />
7 <expand macro="macro_stdio" />
8 <version_command>echo "@VERSION@"</version_command>
9 <command detect_errors="aggressive">
10 <![CDATA[
11 python '$__tool_directory__/anndata_to_csv.py'
12 --inputs '$inputs'
13 --outfile '$outfile'
14
15 ]]>
16 </command>
17 <configfiles>
18 <inputs name="inputs" data_style="paths"/>
19 </configfiles>
20 <inputs>
21 <param name="anndata" type="data" format="h5ad" label="Select the input anndata" />
22 <param name="layer" type="select" label="Select the Anndata layer to export">
23 <option value="x">adata.X</option>
24 <option value="raw">adata.raw.X</option>
25 </param>
26 <param name="cellid" type="text" value="CellID" label="Name of column containing Cell IDs" />
27 </inputs>
28 <outputs>
29 <data format="csv" name="outfile" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="anndata" value="tutorial_data.h5ad" />
34 <param name="layer" value="x" />
35 <output name="outfile" ftype="csv">
36 <assert_contents>
37 <has_n_columns n="41" sep="," />
38 <has_n_lines n="500" />
39 </assert_contents>
40 </output>
41 </test>
42 </tests>
43 <help>
44 <![CDATA[
45 **What it does**
46
47 This scimap function converts from Anndata format to CSV.
48 There are three options for the data matrix returned:
49 1) the current contents of adata.X
50 2) the current contents of adata.raw.X
51 3) the current contents of adata.raw.X with a log+1 transformation applied
52
53 ]]>
54 </help>
55 <expand macro="citations" />
56 </tool>