Mercurial > repos > iuc > scanpy_normalize

comparison macros.xml @ 15:60ec5ecda776 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit c3d9d45e910ef2fad8a85e5f08c8122059a45634
author iuc
date Thu, 19 Sep 2024 06:41:25 +0000
parents 381401225cbc
children c342d700fbc2
comparison
equal deleted inserted replaced
14:381401225cbc 15:60ec5ecda776
7 <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">scanpy</requirement>
8 <requirement type="package" version="0.10.3">anndata</requirement> 8 <requirement type="package" version="0.10.3">anndata</requirement>
9 <requirement type="package" version="1.26.4">numpy</requirement> 9 <requirement type="package" version="1.26.4">numpy</requirement>
10 <requirement type="package" version="2.2.2">pandas</requirement> 10 <requirement type="package" version="2.2.2">pandas</requirement>
11 <requirement type="package" version="1.14.1">scipy</requirement> 11 <requirement type="package" version="1.14.1">scipy</requirement>
12 <requirement type="package" version="0.14.2">statsmodels</requirement> 12 <requirement type="package" version="0.14.2">statsmodels</requirement>
13 <yield /> 13 <yield />
14 </requirements> 14 </requirements>
15 </xml> 15 </xml>
16 <xml name="bio_tools"> 16 <xml name="bio_tools">
17 <xrefs> 17 <xrefs>
27 <citations> 27 <citations>
28 <citation type="doi">10.1186/s13059-017-1382-0</citation> 28 <citation type="doi">10.1186/s13059-017-1382-0</citation>
29 <citation type="doi">10.1093/gigascience/giaa102</citation> 29 <citation type="doi">10.1093/gigascience/giaa102</citation>
30 </citations> 30 </citations>
31 </xml> 31 </xml>
32 32
33 33
34 <!-- param macros --> 34 <!-- param macros -->
35 <xml name="sanitize_query" token_validinitial="string.printable"> 35 <xml name="sanitize_query" token_validinitial="string.printable">
36 <sanitizer> 36 <sanitizer>
37 <valid initial="@VALIDINITIAL@"> 37 <valid initial="@VALIDINITIAL@">
38 <remove value="&apos;"/> 38 <remove value="&apos;"/>
43 <sanitizer> 43 <sanitizer>
44 <valid initial="@VALIDINITIAL@"> 44 <valid initial="@VALIDINITIAL@">
45 <add value=","/> 45 <add value=","/>
46 </valid> 46 </valid>
47 </sanitizer> 47 </sanitizer>
48 </xml> 48 </xml>
49 <xml name="inputs_anndata"> 49 <xml name="inputs_anndata">
50 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/> 50 <param name="adata" type="data" format="h5ad" label="Annotated data matrix"/>
51 </xml> 51 </xml>
52 <xml name="inputs_common_advanced"> 52 <xml name="inputs_common_advanced">
53 <section name="advanced_common" title="Advanced Options" expanded="false"> 53 <section name="advanced_common" title="Advanced Options" expanded="false">
59 <yield /> 59 <yield />
60 </data> 60 </data>
61 <data name="hidden_output" format="txt" label="Log file" > 61 <data name="hidden_output" format="txt" label="Log file" >
62 <filter>advanced_common['show_log']</filter> 62 <filter>advanced_common['show_log']</filter>
63 </data> 63 </data>
64 </xml> 64 </xml>
65 <xml name="param_use_rep"> 65 <xml name="param_use_rep">
66 <param argument="use_rep" type="text" value="" optional="true" label="Use the indicated representation" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter"> 66 <param argument="use_rep" type="text" value="" optional="true" label="Use the indicated representation" help="If not set, the representation is chosen automatically: for n_vars below 50, X is used, otherwise X_pca (uns) is used. If X_pca is not present, it's computed with default parameter">
67 <expand macro="sanitize_query"/> 67 <expand macro="sanitize_query"/>
68 </param> 68 </param>
69 </xml> 69 </xml>
544 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/> 544 <param argument="arrows" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Show arrows?" help="It requires to run 'tl.rna_velocity' before."/>
545 </xml> 545 </xml>
546 <!-- param macros --> 546 <!-- param macros -->
547 547
548 548
549 549
550 <!-- command macros --> 550 <!-- command macros -->
551 <xml name="version_command"> 551 <xml name="version_command">
552 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command> 552 <version_command><![CDATA[python -c "import scanpy as sc;print('scanpy version: %s' % sc.__version__)"]]></version_command>
553 </xml> 553 </xml>
554 <token name="@CMD_PRETTIFY_STDOUT@"><![CDATA[ 554 <token name="@CMD_PRETTIFY_STDOUT@"><![CDATA[
934 size=$method.violin_plot.stripplot.jitter.size, 934 size=$method.violin_plot.stripplot.jitter.size,
935 #end if 935 #end if
936 #end if 936 #end if
937 ]]> 937 ]]>
938 </token> 938 </token>
939 939
940 <xml name="params_seaborn_violinplot"> 940 <xml name="params_seaborn_violinplot">
941 <section name="seaborn_violinplot" title="Parameters for seaborn.violinplot"> 941 <section name="seaborn_violinplot" title="Parameters for seaborn.violinplot">
942 <param argument="bw_method" type="select" label="Name of a reference rule when computing the kernel bandwidth"> 942 <param argument="bw_method" type="select" label="Name of a reference rule when computing the kernel bandwidth">
943 <option value="scott" selected="true">scott</option> 943 <option value="scott" selected="true">scott</option>
944 <option value="silverman">silverman</option> 944 <option value="silverman">silverman</option>
967 #if $method.seaborn_violinplot.color: 967 #if $method.seaborn_violinplot.color:
968 color='$method.seaborn_violinplot.color', 968 color='$method.seaborn_violinplot.color',
969 #end if 969 #end if
970 saturation=$method.seaborn_violinplot.saturation, 970 saturation=$method.seaborn_violinplot.saturation,
971 ]]></token> 971 ]]></token>
972 972
973 <xml name="param_color"> 973 <xml name="param_color">
974 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'"> 974 <param argument="color" type="text" value="" optional="true" label="Keys for annotations of observations/cells or variables/genes" help="One or a list of comma-separated index or key from either '.obs' or '.var'">
975 <expand macro="sanitize_query"/> 975 <expand macro="sanitize_query"/>
976 </param> 976 </param>
977 </xml> 977 </xml>
1015 #end for 1015 #end for
1016 components=$components, 1016 components=$components,
1017 #end if 1017 #end if
1018 ]]> 1018 ]]>
1019 </token> 1019 </token>
1020 1020
1021 <xml name="param_legend_fontsize"> 1021 <xml name="param_legend_fontsize">
1022 <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size"/> 1022 <param argument="legend_fontsize" type="integer" optional="true" value="" label="Legend font size"/>
1023 </xml> 1023 </xml>
1024 <token name="@CMD_PARAM_LEGEND_FONTSIZE@"><![CDATA[ 1024 <token name="@CMD_PARAM_LEGEND_FONTSIZE@"><![CDATA[
1025 #if str($method.plot.legend_fontsize) != '': 1025 #if str($method.plot.legend_fontsize) != '':