Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

comparison macros.xml @ 19:cb43c5d3acd3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 0f11c0478793eaafc7d3bd2e7916ee546528b45f
author iuc
date Thu, 03 Oct 2024 22:42:14 +0000
parents 38db3fef7aad
children 8983e7a04ba7
comparison
equal deleted inserted replaced
18:38db3fef7aad 19:cb43c5d3acd3
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.10.2</token> 2 <token name="@TOOL_VERSION@">1.10.2</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">1</token>
4 <token name="@PROFILE@">21.09</token> 4 <token name="@PROFILE@">21.09</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
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 <requirement type="package" version="0.3.5">fa2</requirement>
13 <yield /> 14 <yield />
14 </requirements> 15 </requirements>
15 </xml> 16 </xml>
16 <xml name="bio_tools"> 17 <xml name="bio_tools">
17 <xrefs> 18 <xrefs>
585 adata, 586 adata,
586 save='.$format', 587 save='.$format',
587 ]]> 588 ]]>
588 </token> 589 </token>
589 <token name="@CMD_SHOW_NONE@"><![CDATA[ 590 <token name="@CMD_SHOW_NONE@"><![CDATA[
590 show=None 591 show=None
591 ]]> 592 ]]>
592 </token> 593 </token>
593 <token name="@CMD_VAR_NAMES_HEADER_CHECK@"><![CDATA[ 594 <token name="@CMD_VAR_NAMES_HEADER_CHECK@"><![CDATA[
594 header='infer' 595 header='infer'
595 #if $method.var_names.type == 'customfile' and $method.var_names.header == 'not_included' : 596 #if $method.var_names.type == 'customfile' and $method.var_names.header == 'not_included' :
1195 <expand macro="options_layout"/> 1196 <expand macro="options_layout"/>
1196 </param> 1197 </param>
1197 </xml> 1198 </xml>
1198 <xml name="params_pl_paga"> 1199 <xml name="params_pl_paga">
1199 <param argument="threshold" type="float" min="0" value="" optional="true" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/> 1200 <param argument="threshold" type="float" min="0" value="" optional="true" label="Threshold to draw edges" help="Do not draw edges for weights below this threshold. Set to 0 if you want all edges. Discarding low-connectivity edges helps in getting a much clearer picture of the graph."/>
1200 <expand macro="param_groups"/> 1201 <param argument="labels" type="text" value="" optional="true" label="The node labels" help="This defaults to the group labels stored in the categorical for which paga() has been computed">
1202 <expand macro="sanitize_query"/>
1203 </param>
1201 <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'."> 1204 <param argument="color" type="text" value="" label="The node colors" help="Gene name or obs. annotation, and also plots the degree of the abstracted graph when passing 'degree_dashed', 'degree_solid'.">
1202 <expand macro="sanitize_query"/> 1205 <expand macro="sanitize_query"/>
1203 </param> 1206 </param>
1204 <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing"/> 1207 <param argument="pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for drawing"/>
1205 <param argument="labels" type="text" value="" label="Comma-separated node labels" help="If none is provided, this defaults to the group labels stored in the categorical for which 'tl.paga' has been computed.">
1206 <expand macro="sanitize_query"/>
1207 </param>
1208 <expand macro="param_layout"/> 1208 <expand macro="param_layout"/>
1209 <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout"/> 1209 <param argument="init_pos" type="data" format="tabular,csv,tsv" optional="true" label="Two-column tabular file storing the x and y coordinates for initializing the layout"/>
1210 <param argument="random_state" type="integer" value="0" label="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If 'None', the initial state is not reproducible."/> 1210 <param argument="random_state" type="integer" value="0" label="For layouts with random initialization like 'fr', change this to use different intial states for the optimization. If 'None', the initial state is not reproducible."/>
1211 <param argument="root" type="text" value="0" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is 'None' or an empty list, the root vertices are automatically calculated based on topological sorting."> 1211 <param argument="root" type="text" value="0" label="Comma-separated roots" help="If choosing a tree layout, this is the index of the root node or a list of root node indices. If this is a non-empty vector then the supplied node IDs are used as the roots of the trees (or a single tree if the graph is connected). If this is 'None' or an empty list, the root vertices are automatically calculated based on topological sorting.">
1212 <expand macro="sanitize_query"/> 1212 <expand macro="sanitize_query"/>
1235 </xml> 1235 </xml>
1236 <token name="@CMD_PARAMS_PL_PAGA@"><![CDATA[ 1236 <token name="@CMD_PARAMS_PL_PAGA@"><![CDATA[
1237 #if str($method.threshold) != '': 1237 #if str($method.threshold) != '':
1238 threshold=$method.threshold, 1238 threshold=$method.threshold,
1239 #end if 1239 #end if
1240 #if str($method.groups) != '': 1240 #if str($method.labels) != '':
1241 #set $groups=([x.strip() for x in str($method.groups).split(',')]) 1241 #set $labels=([x.strip() for x in str($method.labels).split(',')])
1242 groups=$groups, 1242 labels=$labels,
1243 #end if 1243 #end if
1244 #if str($method.color) != '': 1244 #if str($method.color) != '':
1245 #set $color=([x.strip() for x in str($method.color).split(',')]) 1245 #set $color=([x.strip() for x in str($method.color).split(',')])
1246 color=$color, 1246 color=$color,
1247 #end if 1247 #end if
1248 #if $method.pos: 1248 #if $method.pos:
1249 pos=np.fromfile($method.pos, dtype=dt), 1249 pos=np.fromfile($method.pos, dtype=dt),
1250 #end if
1251 #if str($method.labels) != '':
1252 #set $labels=([x.strip() for x in str($method.labels).split(',')])
1253 labels=$labels,
1254 #end if 1250 #end if
1255 layout='$method.layout', 1251 layout='$method.layout',
1256 #if $method.init_pos: 1252 #if $method.init_pos:
1257 init_pos=np.fromfile($method.init_pos, dtype=dt), 1253 init_pos=np.fromfile($method.init_pos, dtype=dt),
1258 #end if 1254 #end if
1267 solid_edges='$method.solid_edges', 1263 solid_edges='$method.solid_edges',
1268 #if str($method.dashed_edges) != '': 1264 #if str($method.dashed_edges) != '':
1269 dashed_edges='$method.dashed_edges', 1265 dashed_edges='$method.dashed_edges',
1270 #end if 1266 #end if
1271 single_component=$method.single_component, 1267 single_component=$method.single_component,
1268 #if str($method.fontsize) != '':
1272 fontsize=$method.fontsize, 1269 fontsize=$method.fontsize,
1270 #end if
1273 node_size_scale=$method.node_size_scale, 1271 node_size_scale=$method.node_size_scale,
1274 node_size_power=$method.node_size_power, 1272 node_size_power=$method.node_size_power,
1275 edge_width_scale=$method.edge_width_scale, 1273 edge_width_scale=$method.edge_width_scale,
1276 #if str($method.min_edge_width) != '': 1274 #if str($method.min_edge_width) != '':
1277 min_edge_width=$method.min_edge_width, 1275 min_edge_width=$method.min_edge_width,