Mercurial > repos > ebi-gxa > scanpy_filter_genes
comparison scanpy-filter-genes.xml @ 5:f1e4de78d768 draft
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 |
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date | Wed, 20 Nov 2019 05:15:47 -0500 |
parents | fa6c08064fc1 |
children | cb55f68ea1d7 |
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4:fa6c08064fc1 | 5:f1e4de78d768 |
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1 <?xml version="1.0" encoding="utf-8"?> | 1 <?xml version="1.0" encoding="utf-8"?> |
2 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy3"> | 2 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy0"> |
3 <description>based on counts and numbers of cells expressed</description> | 3 <description>based on counts and numbers of cells 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"/> |
11 #if $parameters | 11 #if $parameters |
12 #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters]) | 12 #set pars = ' '.join(['--param g:{name} {min} {max}'.format(**$p) for $p in $parameters]) |
13 ${pars} | 13 ${pars} |
14 #end if | 14 #end if |
15 #if $categories | 15 #if $categories |
16 #set cats = ' '.join(['--category g:{name} {values}'.format(**$c) for $c in $categories]) | 16 #set cats = ' '.join(["--category g:{name} '{negate}{values}'".format(**$c) for $c in $categories]) |
17 ${cats} | 17 ${cats} |
18 #end if | 18 #end if |
19 #if $subsets | 19 #if $subsets |
20 #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets]) | 20 #set subs = ' '.join(['--subset g:{name} {subset}'.format(**$s) for $s in $subsets]) |
21 ${subs} | 21 ${subs} |
38 <param name="max" type="float" min="0" value="1e9" label="Max value"/> | 38 <param name="max" type="float" min="0" value="1e9" label="Max value"/> |
39 </repeat> | 39 </repeat> |
40 | 40 |
41 <repeat name="categories" title="Categories used to filter genes" min="0"> | 41 <repeat name="categories" title="Categories used to filter genes" min="0"> |
42 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> | 42 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> |
43 <param name="values" type="text" value="" label="Comma-separated values to keep"/> | 43 <param name="values" type="text" value="" label="Comma-separated list of categories"/> |
44 <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."/> | |
44 </repeat> | 45 </repeat> |
45 | 46 |
46 <repeat name="subsets" title="Subsets used to filter genes" min="0"> | 47 <repeat name="subsets" title="Subsets used to filter genes" min="0"> |
47 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> | 48 <param name="name" type="text" value="" label="Name of the categorical variable to filter on"/> |
48 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/> | 49 <param name="subset" type="data" format="tabular" label="List of values to keep" help="A one-column headerless text file is required"/> |