Mercurial > repos > iuc > qualimap_bamqc

comparison qualimap_bamqc.xml @ 3:5f8e69cc4c6e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875"
author iuc
date Sat, 16 May 2020 09:47:55 -0400
parents 4a89c6f84425
children 19ece8afbaab
comparison
equal deleted inserted replaced
2:e7fd6754d093 3:5f8e69cc4c6e
1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy1"> 1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy2">
2 <macros> 2 <macros>
3 <import>qualimap_macros.xml</import> 3 <import>qualimap_macros.xml</import>
4 </macros> 4 </macros>
5 <expand macro="requirements" /> 5 <expand macro="requirements" />
6 <expand macro="version_command" /> 6 <expand macro="version_command" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 #import os 8 #import os
9 #import re
9 @SET_JAVA_OPTS@ && 10 @SET_JAVA_OPTS@ &&
10 11
11 ## Set some default file names and paths 12 ## Set some default file names and paths
12 ## where we expect tool output to end up. 13 ## where we expect tool output to end up.
13 ## Note that most of these need to be overwritten if the user is 14 ## Note that most of these need to be overwritten if the user is
37 #set $per_base_coverage_target = '/dev/null' 38 #set $per_base_coverage_target = '/dev/null'
38 #end if 39 #end if
39 #end if 40 #end if
40 #end if 41 #end if
41 42
43 #set input_name = re.sub('[^\s\w\-]', '_', str($input1.name))
44 ln -s '$input1' '$input_name' &&
45
42 qualimap bamqc 46 qualimap bamqc
43 -bam '$input1' -outdir results -outformat html 47 -bam '$input_name' -outdir results -outformat html
44 --collect-overlap-pairs 48 --collect-overlap-pairs
45 #if str($stats_regions.region_select) == 'custom_regions': 49 #if str($stats_regions.region_select) == 'custom_regions':
46 -gff ${regions_file} ${stats_regions.outside_stats} 50 -gff ${regions_file} ${stats_regions.outside_stats}
47 #end if 51 #end if
48 #if $per_base_coverage: 52 #if $per_base_coverage: