Mercurial > repos > iuc > episcanpy_preprocess

comparison macros.xml @ 0:8ba672d0d8aa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/episcanpy/ commit ce8ee43d7285503a24c7b0f55c09c513be8c66f5
author iuc
date Tue, 18 Apr 2023 13:18:50 +0000
parents
children 29f5f25b9935
comparison
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-1:000000000000 0:8ba672d0d8aa
1 <macros>
2 <token name="@TOOL_VERSION@">0.3.2</token>
3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">21.01</token>
5 <xml name="requirements">
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">episcanpy</requirement>
8 <requirement type="package" version="1.0.8">bzip2</requirement>
9 <requirement type="package" version="1.11">tabix</requirement>
10 <requirement type="package" version="0.7.5">anndata</requirement>
11 <requirement type="package" version="0.8.3">leidenalg</requirement>
12 <requirement type="package" version="0.8.0">louvain</requirement>
13 <yield />
14 </requirements>
15 </xml>
16 <xml name="bio_tools">
17 <xrefs>
18 <xref type="bio.tools">episcanpy</xref>
19 </xrefs>
20 </xml>
21 <xml name="citations">
22 <citations>
23 <citation type="doi">10.1038/s41467-021-25131-3</citation>
24 </citations>
25 </xml>
26 <xml name="version_command">
27 <version_command><![CDATA[python -c "import episcanpy as esc; print(f'{esc.__version__}')"]]></version_command>
28 </xml>
29 <token name="@CMD@"><![CDATA[
30 cp '$adata' 'anndata.h5ad' &&
31 cat '$script_file' > '$hidden_output' &&
32 python '$script_file' >> '$hidden_output' &&
33 touch 'anndata_info.txt' &&
34 cat 'anndata_info.txt' @CMD_prettify_stdout@
35 ]]>
36 </token>
37 <token name="@CMD_imports@"><![CDATA[
38 import episcanpy as esc
39 import pandas as pd
40 import numpy as np
41 ]]>
42 </token>
43 <xml name="sanitize_query" token_validinitial="string.printable">
44 <sanitizer>
45 <valid initial="@VALIDINITIAL@">
46 <remove value="&apos;" />
47 </valid>
48 </sanitizer>
49 </xml>
50 <xml name="sanitize_vectors" token_validinitial="string.digits">
51 <sanitizer>
52 <valid initial="@VALIDINITIAL@">
53 <add value=","/>
54 </valid>
55 </sanitizer>
56 </xml>
57 <xml name="inputs_anndata">
58 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
59 </xml>
60 <token name="@CMD_read_inputs@"><![CDATA[
61 adata = esc.read('anndata.h5ad')
62 ]]>
63 </token>
64 <xml name="inputs_common_advanced">
65 <section name="advanced_common" title="Advanced Options" expanded="false">
66 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
67 </section>
68 </xml>
69 <xml name="anndata_outputs">
70 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
71 <data name="hidden_output" format="txt" label="Log file" hidden="true">
72 <filter>advanced_common['show_log']</filter>
73 </data>
74 </xml>
75 <token name="@CMD_anndata_write_outputs@"><![CDATA[
76 adata.write('anndata.h5ad')
77 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
78 print(adata, file=ainfo)
79 ]]></token>
80 <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'
81 ]]></token>
82 <xml name="coverage_params">
83 <param argument="binary" type="boolean" truevalue="True" falsevalue="False" checked="false"
84 label="Binarized matrix?" help="To reduce computing time, you can specify if the matrix is already binary" />
85 <param argument="log" type="boolean" truevalue="True" falsevalue="False" checked="false"
86 label="Log transform?" />
87 <param argument="threshold" type="float" min="0" value="" label="Minimum number of cells or minimumn number of features to be indicated in the plot"
88 help="For coverage cells, please use min number of features and for coverage features, use min number of cells."/>
89 <param argument="bins" type="integer" min="0" value="50" label="Number of bins in the output histogram plot"/>
90 </xml>
91 <xml name="param_plot_format">
92 <param name="format" type="select" label="Format for saving figures">
93 <option value="png">png</option>
94 <option value="pdf">pdf</option>
95 <option value="svg">svg</option>
96 </param>
97 </xml>
98 </macros>