Mercurial > repos > iuc > scanpy_cluster_reduce_dimension

comparison macros.xml @ 8:35bc2eb568ed draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 7b8af82cb8a3438d2a6535986e357527e5c6efec"
author iuc
date Tue, 16 Mar 2021 13:03:42 +0000
parents b2df381a6004
children aaa5da8e73a9
comparison
equal deleted inserted replaced
7:b2df381a6004 8:35bc2eb568ed
1 <macros> 1 <macros>
2 <token name="@version@">1.4.4.post1</token> 2 <token name="@version@">1.7.1</token>
3 <token name="@profile@">19.01</token> 3 <token name="@profile@">19.01</token>
4 <token name="@galaxy_version@"><![CDATA[@version@+galaxy3]]></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="2.0.17">loompy</requirement>
9 <requirement type="package" version="2.9.0">h5py</requirement> 9 <requirement type="package" version="0.8.3">leidenalg</requirement>
10 <requirement type="package" version="0.7.0">leidenalg</requirement>
11 <yield /> 10 <yield />
12 </requirements> 11 </requirements>
13 </xml> 12 </xml>
14 <xml name="citations"> 13 <xml name="citations">
15 <citations> 14 <citations>
27 touch 'anndata_info.txt' && 26 touch 'anndata_info.txt' &&
28 cat 'anndata_info.txt' @CMD_prettify_stdout@ 27 cat 'anndata_info.txt' @CMD_prettify_stdout@
29 ]]> 28 ]]>
30 </token> 29 </token>
31 <token name="@CMD_imports@"><![CDATA[ 30 <token name="@CMD_imports@"><![CDATA[
32 import sys
33 sys.stderr = open('$hidden_output', 'a')
34
35 import scanpy as sc 31 import scanpy as sc
36 import pandas as pd 32 import pandas as pd
37 import numpy as np 33 import numpy as np
38 ]]> 34 ]]>
39 </token> 35 </token>
766 </param> 762 </param>
767 <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/> 763 <param argument="linewidth" type="float" value="0" label="Width of the gray lines that frame the plot elements" help=""/>
768 <param argument="color" type="select" label="Color for all of the elements" help=""> 764 <param argument="color" type="select" label="Color for all of the elements" help="">
769 <expand macro="matplotlib_color"/> 765 <expand macro="matplotlib_color"/>
770 </param> 766 </param>
771 <param argument="palette" type="select" label="Colors to use for the different levels of the hue variable" help="">
772 <expand macro="matplotlib_pyplot_colormap"/>
773 </param>
774 <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/> 767 <param argument="saturation" type="float" value="0.75" min="0" max="1" label="Proportion of the original saturation to draw colors at" help=""/>
775 </section> 768 </section>
776 </xml> 769 </xml>
777 <token name="@CMD_params_seaborn_violinplot@"><![CDATA[ 770 <token name="@CMD_params_seaborn_violinplot@"><![CDATA[
778 bw='$method.seaborn_violinplot.bw', 771 bw='$method.seaborn_violinplot.bw',
779 #if $method.seaborn_violinplot.orient 772 #if $method.seaborn_violinplot.orient
780 orient='$method.seaborn_violinplot.orient', 773 orient='$method.seaborn_violinplot.orient',
781 #end if 774 #end if
782 linewidth=$method.seaborn_violinplot.linewidth, 775 linewidth=$method.seaborn_violinplot.linewidth,
783 color='$method.seaborn_violinplot.color', 776 color='$method.seaborn_violinplot.color',
784 palette='$method.seaborn_violinplot.palette',
785 saturation=$method.seaborn_violinplot.saturation 777 saturation=$method.seaborn_violinplot.saturation
786 ]]></token> 778 ]]></token>
787 <xml name="param_color"> 779 <xml name="param_color">
788 <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'"> 780 <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'">
789 <expand macro="sanitize_query" /> 781 <expand macro="sanitize_query" />
1003 <option value="drl">drl: Distributed Recursive Layout, pretty fast</option> 995 <option value="drl">drl: Distributed Recursive Layout, pretty fast</option>
1004 <option value="rt">rt: Reingold Tilford tree layout</option> 996 <option value="rt">rt: Reingold Tilford tree layout</option>
1005 <option value="eq_tree">eq_tree: Equally spaced tree</option> 997 <option value="eq_tree">eq_tree: Equally spaced tree</option>
1006 </xml> 998 </xml>
1007 <xml name="param_layout"> 999 <xml name="param_layout">
1008 <param argument="layout" type="select" label="Plotting layout" help=""> 1000 <param argument="layout" type="select" label="Plotting layout" optional="false" help="">
1009 <expand macro="options_layout"/> 1001 <expand macro="options_layout"/>
1010 </param> 1002 </param>
1011 </xml> 1003 </xml>
1012 <xml name="param_root"> 1004 <xml name="param_root">
1013 <param argument="root" type="text" value="" 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."> 1005 <param argument="root" type="text" value="" 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.">