Mercurial > repos > ebi-gxa > scanpy_filter_genes
comparison scanpy-filter-genes.xml @ 7:0bba942e0869 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 06:32:34 -0500 |
parents | cb55f68ea1d7 |
children | 88bccd53d18a |
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6:cb55f68ea1d7 | 7:0bba942e0869 |
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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@+galaxy4"> | 2 <tool id="scanpy_filter_genes" name="Scanpy FilterGenes" version="@TOOL_VERSION@+galaxy5"> |
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"/> |
8 <command detect_errors="exit_code"><![CDATA[ | 8 <command detect_errors="exit_code"><![CDATA[ |
9 ln -s '${input_obj_file}' input.h5 && | 9 ln -s '${input_obj_file}' input.h5 && |
10 PYTHONIOENCODING=utf-8 scanpy-filter-genes | 10 PYTHONIOENCODING=utf-8 scanpy-filter-genes |
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 $categories |
16 #set cats = ' '.join(["--category g:{name} '{negate}{values}'".format(**$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} |
22 #end if | 22 #end if |
23 @INPUT_OPTS@ | 23 @INPUT_OPTS@ |
24 @OUTPUT_OPTS@ | 24 @OUTPUT_OPTS@ |
25 @EXPORT_MTX_OPTS@ | 25 @EXPORT_MTX_OPTS@ |