Mercurial > repos > iuc > scanpy_normalize

comparison macros.xml @ 6:3bcd5445cd7a draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 5a90fd345b43ca12366f4475f4cfd88ef197e452"
author iuc
date Thu, 20 Feb 2020 08:24:54 -0500
parents 55f2212bb675
children a407e7f8bdc1
comparison
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5:ec32793ce1dd 6:3bcd5445cd7a
19 <xml name="version_command"> 19 <xml name="version_command">
20 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command> 20 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
21 </xml> 21 </xml>
22 <token name="@CMD@"><![CDATA[ 22 <token name="@CMD@"><![CDATA[
23 cp '$adata' 'anndata.h5ad' && 23 cp '$adata' 'anndata.h5ad' &&
24 cat '$script_file' && 24 cat '$script_file' > '$hidden_output' &&
25 python '$script_file' && 25 python '$script_file' >> '$hidden_output' &&
26 ls . 26 ls . >> '$hidden_output' &&
27 touch 'anndata_info.txt' &&
28 cat 'anndata_info.txt' @CMD_prettify_stdout@
27 ]]> 29 ]]>
28 </token> 30 </token>
29 <token name="@CMD_imports@"><![CDATA[ 31 <token name="@CMD_imports@"><![CDATA[
32 import sys
33 sys.stderr = open('$hidden_output', 'a')
34
30 import scanpy as sc 35 import scanpy as sc
31 import pandas as pd 36 import pandas as pd
32 import numpy as np 37 import numpy as np
33 ]]> 38 ]]>
34 </token> 39 </token>
37 </xml> 42 </xml>
38 <token name="@CMD_read_inputs@"><![CDATA[ 43 <token name="@CMD_read_inputs@"><![CDATA[
39 adata = sc.read('anndata.h5ad') 44 adata = sc.read('anndata.h5ad')
40 ]]> 45 ]]>
41 </token> 46 </token>
47 <xml name="inputs_common_advanced">
48 <section name="advanced_common" title="Advanced Options" expanded="false">
49 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
50 </section>
51 </xml>
42 <xml name="anndata_outputs"> 52 <xml name="anndata_outputs">
43 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/> 53 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
54 <data name="hidden_output" format="txt" label="Log file" >
55 <filter>advanced_common['show_log']</filter>
56 </data>
44 </xml> 57 </xml>
45 <token name="@CMD_anndata_write_outputs@"><![CDATA[ 58 <token name="@CMD_anndata_write_outputs@"><![CDATA[
46 adata.write('anndata.h5ad') 59 adata.write('anndata.h5ad')
60 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
61 print(adata, file=ainfo)
47 ]]> 62 ]]>
48 </token> 63 </token>
64 <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'
65 ]]></token>
49 <xml name="svd_solver"> 66 <xml name="svd_solver">
50 <param name="svd_solver" type="select" label="SVD solver to use" help=""> 67 <param name="svd_solver" type="select" label="SVD solver to use" help="">
51 <option value="auto">Automatically chosen depending on the size of the problem</option> 68 <option value="auto">Automatically chosen depending on the size of the problem</option>
52 <option value="arpack">ARPACK wrapper in SciPy</option> 69 <option value="arpack">ARPACK wrapper in SciPy</option>
53 <option value="randomized">Randomized algorithm due to Halko (2009)</option> 70 <option value="randomized">Randomized algorithm due to Halko (2009)</option>