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comparison scanpy-filter-cells.xml @ 4:1b0fdf08a454 draft

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1d069e25584e436d7628694cb8853a15f1f85604
author ebi-gxa
date Wed, 20 Nov 2019 05:18:49 -0500
parents 8e48fa9618c1
children 9b2072ee4bdd
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3:8e48fa9618c1 4:1b0fdf08a454
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy1"> 2 <tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy0">
3 <description>based on counts and numbers of genes expressed</description> 3 <description>based on counts and numbers of genes expressed</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
14 #if $parameters 14 #if $parameters
15 #set pars = ' '.join(['--param c:{name} {min} {max}'.format(**$p) for $p in $parameters]) 15 #set pars = ' '.join(['--param c:{name} {min} {max}'.format(**$p) for $p in $parameters])
16 ${pars} 16 ${pars}
17 #end if 17 #end if
18 #if $categories 18 #if $categories
19 #set cats = ' '.join(['--category c:{name} {values}'.format(**$c) for $c in $categories]) 19 #set cats = ' '.join(["--category c:{name} '{negate}{values}'".format(**$c) for $c in $categories])
20 ${cats} 20 ${cats}
21 #end if 21 #end if
22 #if $subsets 22 #if $subsets
23 #set subs = ' '.join(['--subset c:{name} {subset}'.format(**$s) for $s in $subsets]) 23 #set subs = ' '.join(['--subset c:{name} {subset}'.format(**$s) for $s in $subsets])
24 ${subs} 24 ${subs}
45 <param name="max" type="float" value="1e9" label="Max value"/> 45 <param name="max" type="float" value="1e9" label="Max value"/>
46 </repeat> 46 </repeat>
47 47
48 <repeat name="categories" title="Categories used to filter cells" min="0"> 48 <repeat name="categories" title="Categories used to filter cells" min="0">
49 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> 49 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
50 <param name="values" type="text" value="" label="Comma-separated values to keep"/> 50 <param name="values" type="text" value="" label="Comma-separated list of categories"/>
51 <param name="negate" type="boolean" truevalue="!" falsevalue="" checked="false" label="Apply as negative filter" help="If enabled, specified categories will be removed rather than retained."/>
51 </repeat> 52 </repeat>
52 53
53 <repeat name="subsets" title="Subsets used to filter cells" min="0"> 54 <repeat name="subsets" title="Subsets used to filter cells" min="0">
54 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> 55 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/>
55 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/> 56 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/>