Mercurial > repos > ebi-gxa > scanpy_filter_cells
comparison scanpy-filter-cells.xml @ 6:9024cf7a9a13 draft
planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 0a162684a5859a53eefb14af11ba8ec64d42b213-dirty
author | ebi-gxa |
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date | Wed, 20 Nov 2019 06:36:04 -0500 |
parents | 9b2072ee4bdd |
children | 9c65f1de489b |
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5:9b2072ee4bdd | 6:9024cf7a9a13 |
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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_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy2"> | 2 <tool id="scanpy_filter_cells" name="Scanpy FilterCells" version="@TOOL_VERSION@+galaxy3"> |
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"/> |
10 PYTHONIOENCODING=utf-8 scanpy-filter-cells | 10 PYTHONIOENCODING=utf-8 scanpy-filter-cells |
11 #if $gene_name | 11 #if $gene_name |
12 --gene-name '${gene_name}' | 12 --gene-name '${gene_name}' |
13 #end if | 13 #end if |
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 $categories |
19 #set cats = ' '.join(["--category c:{name} '{negate}{values}'".format(**$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} |
25 #end if | 25 #end if |
26 @INPUT_OPTS@ | 26 @INPUT_OPTS@ |
27 @OUTPUT_OPTS@ | 27 @OUTPUT_OPTS@ |
28 @EXPORT_MTX_OPTS@ | 28 @EXPORT_MTX_OPTS@ |