Mercurial > repos > iuc > scanpy_remove_confounders

comparison macros.xml @ 11:73ab2ac53d06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit aba2a85f5da6e1094f382d1f0d94c4b8f2544a7d
author iuc
date Wed, 08 Nov 2023 14:45:35 +0000
parents bf2017df9837
children 458e8f43a775
comparison
equal deleted inserted replaced
10:bf2017df9837 11:73ab2ac53d06
1 <macros> 1 <macros>
2 <token name="@version@">1.7.1</token> 2 <token name="@version@">1.9.6</token>
3 <token name="@profile@">19.01</token> 3 <token name="@profile@">22.05</token>
4 <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token> 4 <token name="@galaxy_version@"><![CDATA[@version@+galaxy0]]></token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@version@">scanpy</requirement> 7 <requirement type="package" version="@version@">scanpy</requirement>
8 <requirement type="package" version="2.0.17">loompy</requirement> 8 <requirement type="package" version="3.0.6">loompy</requirement>
9 <requirement type="package" version="0.8.3">leidenalg</requirement> 9 <requirement type="package" version="0.10.1">leidenalg</requirement>
10 <requirement type="package" version="0.8.1">louvain</requirement>
11 <requirement type="package" version="1.5.3">pandas</requirement>
12 <requirement type="package" version="3.7">matplotlib</requirement>
13 <requirement type="package" version="0.12.2">seaborn</requirement>
10 <yield /> 14 <yield />
11 </requirements> 15 </requirements>
12 </xml> 16 </xml>
13 <xml name="bio_tools"> 17 <xml name="bio_tools">
14 <xrefs> 18 <xrefs>
15 <xref type="bio.tools">scanpy</xref> 19 <xref type="bio.tools">scanpy</xref>
16 </xrefs> 20 </xrefs>
17 </xml> 21 </xml>
22 <xml name="creators">
23 <creator>
24 <organization name="European Galaxy Team" url="https://galaxyproject.org/eu/" />
25 </creator>
26 </xml>
18 <xml name="citations"> 27 <xml name="citations">
19 <citations> 28 <citations>
20 <citation type="doi">10.1186/s13059-017-1382-0</citation> 29 <citation type="doi">10.1186/s13059-017-1382-0</citation>
30 <citation type="doi">10.1093/gigascience/giaa102</citation>
21 </citations> 31 </citations>
22 </xml> 32 </xml>
23 <xml name="version_command"> 33 <xml name="version_command">
24 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command> 34 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
25 </xml> 35 </xml>
54 </xml> 64 </xml>
55 <xml name="inputs_anndata"> 65 <xml name="inputs_anndata">
56 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> 66 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
57 </xml> 67 </xml>
58 <token name="@CMD_read_inputs@"><![CDATA[ 68 <token name="@CMD_read_inputs@"><![CDATA[
59 adata = sc.read('anndata.h5ad') 69 adata = sc.read_h5ad('anndata.h5ad')
60 ]]> 70 ]]>
61 </token> 71 </token>
62 <xml name="inputs_common_advanced"> 72 <xml name="inputs_common_advanced">
63 <section name="advanced_common" title="Advanced Options" expanded="false"> 73 <section name="advanced_common" title="Advanced Options" expanded="false">
64 <param name="show_log" type="boolean" checked="false" label="Output Log?" /> 74 <param name="show_log" type="boolean" checked="false" label="Output Log?" />
65 </section> 75 </section>
66 </xml> 76 </xml>
67 <xml name="anndata_outputs"> 77 <xml name="anndata_outputs">
68 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/> 78 <data name="anndata_out" format="h5ad" from_work_dir="anndata.h5ad" label="${tool.name} (${method.method}) on ${on_string}: Annotated data matrix"/>
69 <data name="hidden_output" format="txt" label="Log file" > 79 <data name="hidden_output" format="txt" label="Log file" >
70 <filter>advanced_common['show_log']</filter> 80 <filter>advanced_common['show_log']</filter>
71 </data> 81 </data>
72 </xml> 82 </xml>
73 <token name="@CMD_anndata_write_outputs@"><![CDATA[ 83 <token name="@CMD_anndata_write_outputs@"><![CDATA[
74 adata.write('anndata.h5ad') 84 adata.write_h5ad('anndata.h5ad')
75 with open('anndata_info.txt','w', encoding='utf-8') as ainfo: 85 with open('anndata_info.txt','w', encoding='utf-8') as ainfo:
76 print(adata, file=ainfo) 86 print(adata, file=ainfo)
77 ]]> 87 ]]>
78 </token> 88 </token>
79 <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' 89 <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'
873 <expand macro="matplotlib_pyplot_colormap"/> 883 <expand macro="matplotlib_pyplot_colormap"/>
874 </param> 884 </param>
875 </xml> 885 </xml>
876 <xml name="param_color_map"> 886 <xml name="param_color_map">
877 <param argument="color_map" type="select" label="Color map to use for continous variables" help=""> 887 <param argument="color_map" type="select" label="Color map to use for continous variables" help="">
878 <option value="None">Default</option> 888 <option value="" >Default</option>
879 <expand macro="matplotlib_pyplot_colormap"/> 889 <expand macro="matplotlib_pyplot_colormap"/>
880 </param> 890 </param>
881 </xml> 891 </xml>
882 <xml name="param_frameon"> 892 <xml name="param_frameon">
883 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/> 893 <param argument="frameon" type="boolean" truevalue="True" falsevalue="False" checked="true" label="Draw a frame around the scatter plot?" help=""/>
977 projection='$method.plot.projection', 987 projection='$method.plot.projection',
978 legend_loc='$method.plot.legend_loc', 988 legend_loc='$method.plot.legend_loc',
979 @CMD_param_legend_fontsize@ 989 @CMD_param_legend_fontsize@
980 legend_fontweight='$method.plot.legend_fontweight', 990 legend_fontweight='$method.plot.legend_fontweight',
981 @CMD_param_size@ 991 @CMD_param_size@
982 #if str($method.plot.color_map) != 'None' 992 #if str($method.plot.color_map) != ''
983 color_map='$method.plot.color_map', 993 color_map='$method.plot.color_map',
984 #end if 994 #end if
985 #if str($method.plot.palette) != '' 995 #if str($method.plot.palette) != ''
986 palette='$method.plot.palette', 996 palette='$method.plot.palette',
987 #end if 997 #end if