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comparison macros.xml @ 0:9d7ccdb258df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cosg/ commit 2e477dea2f014c265e6a2c6d25432d0e2bace733
author iuc
date Wed, 29 May 2024 14:25:02 +0000
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-1:000000000000 0:9d7ccdb258df
1 <macros>
2 <token name="@TOOL_VERSION@">1.0.1</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@profile@">22.05</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">cosg</requirement>
8 <requirement type="package" version="1.9.8">scanpy</requirement>
9 <requirement type="package" version="1.5.3">pandas</requirement>
10 <requirement type="package" version="3.7">matplotlib</requirement>
11 <requirement type="package" version="0.12.2">seaborn</requirement>
12 <yield />
13 </requirements>
14 </xml>
15 <xml name="creators">
16 <creator>
17 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
18 </creator>
19 </xml>
20 <xml name="citations">
21 <citations>
22 <citation type="doi">10.1093/bib/bbab579</citation>
23 <citation type="doi">10.1093/gigascience/giaa102</citation>
24 </citations>
25 </xml>
26 <xml name="version_command">
27 <version_command><![CDATA[python -c "import cosg;import importlib.metadata;print('%s' % importlib.metadata.version('cosg'))"]]></version_command>
28 </xml>
29 <token name="@CMD@"><![CDATA[
30 cp '$adata' 'anndata.h5ad' &&
31 cat '$script_file' > '$hidden_output' &&
32 python '$script_file' >> '$hidden_output' &&
33 ls . >> '$hidden_output' &&
34 touch 'anndata_info.txt' &&
35 cat 'anndata_info.txt' @CMD_prettify_stdout@
36 ]]>
37 </token>
38 <token name="@CMD_imports@"><![CDATA[
39 import scanpy as sc
40 import pandas as pd
41 import numpy as np
42 import cosg
43 ]]>
44 </token>
45 <xml name="sanitize_query" token_validinitial="string.printable">
46 <sanitizer>
47 <valid initial="@VALIDINITIAL@">
48 <remove value="&apos;" />
49 </valid>
50 </sanitizer>
51 </xml>
52 <xml name="sanitize_vectors" token_validinitial="string.digits">
53 <sanitizer>
54 <valid initial="@VALIDINITIAL@">
55 <add value=","/>
56 </valid>
57 </sanitizer>
58 </xml>
59 <xml name="inputs_anndata">
60 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
61 </xml>
62 <token name="@CMD_read_inputs@"><![CDATA[
63 adata = sc.read_h5ad('anndata.h5ad')
64 ]]>
65 </token>
66 <xml name="inputs_common_advanced">
67 <section name="advanced_common" title="Advanced Output Options" expanded="false">
68 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
69 </section>
70 </xml>
71 <xml name="anndata_outputs">
72 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} on ${on_string}: Annotated data matrix"/>
73 <data name="hidden_output" format="txt" label="Log file" >
74 <filter>advanced_common['show_log']</filter>
75 </data>
76 </xml>
77 <token name="@CMD_anndata_write_outputs@"><![CDATA[
78 adata.write_h5ad('anndata.h5ad')
79 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
80 print(adata, file=ainfo)
81 ]]>
82 </token>
83 <token name="@CMD_prettify_stdout@"><![CDATA[ | sed -r '1 s|AnnData object with (.+) = (.*)\s*|\1: \2|g' | sed "s|'||g" | sed -r 's|^\s*(.*):\s(.*)|[\1]\n- \2|g' | sed 's|, |\n- |g'
84 ]]></token>
85 </macros>