Mercurial > repos > iuc > qualimap_bamqc

comparison qualimap_bamqc.xml @ 1:4a89c6f84425 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit 08beeabf7a8e91d0e95f5cdb71249dd6efe2bd46"
author iuc
date Tue, 29 Oct 2019 09:14:20 -0400
parents ac607906f10a
children 5f8e69cc4c6e
comparison
equal deleted inserted replaced
0:ac607906f10a 1:4a89c6f84425
1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@"> 1 <tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy1">
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" />
19 #set $coverage_file = os.path.join($out_dir, 'coverage.txt') 19 #set $coverage_file = os.path.join($out_dir, 'coverage.txt')
20 ## This is the only file path that qualimap does not calculate 20 ## This is the only file path that qualimap does not calculate
21 ## from $out_dir. 21 ## from $out_dir.
22 #set $per_base_coverage_target = $coverage_file 22 #set $per_base_coverage_target = $coverage_file
23 23
24 qualimap bamqc
25 -bam '$input1' -outdir results -outformat html
26 --collect-overlap-pairs
27 #if str($stats_regions.region_select) == 'custom_regions': 24 #if str($stats_regions.region_select) == 'custom_regions':
28 -gff ${stats_regions.regions} 25 ## Have qualimap detect file format by suffix
26 ## since its autodetection is unreliable.
27 #set $regions_file = '.'.join(['regions', str($stats_regions.regions.ext)])
28 ln -s '${stats_regions.regions}' ${regions_file} &&
29
29 #if $stats_regions.outside_stats: 30 #if $stats_regions.outside_stats:
30 #set $report_name = 'qualimapReportOutsideRegions' 31 #set $report_name = 'qualimapReportOutsideRegions'
31 #set $summary_report = 'outside_results.txt' 32 #set $summary_report = 'outside_results.txt'
32 #set $coverage_file = os.path.join( 33 #set $coverage_file = os.path.join(
33 $out_dir, 'outside_coverage.txt' 34 $out_dir, 'outside_coverage.txt'
34 ) 35 )
35 #if $per_base_coverage: 36 #if $per_base_coverage:
36 #set $per_base_coverage_target = '/dev/null' 37 #set $per_base_coverage_target = '/dev/null'
37 #end if 38 #end if
38 ${stats_regions.outside_stats}
39 #end if 39 #end if
40 #end if
41
42 qualimap bamqc
43 -bam '$input1' -outdir results -outformat html
44 --collect-overlap-pairs
45 #if str($stats_regions.region_select) == 'custom_regions':
46 -gff ${regions_file} ${stats_regions.outside_stats}
40 #end if 47 #end if
41 #if $per_base_coverage: 48 #if $per_base_coverage:
42 $per_base_coverage $per_base_coverage_target 49 $per_base_coverage $per_base_coverage_target
43 #end if 50 #end if
44 -nw ${plot_specific.n_bins} 51 -nw ${plot_specific.n_bins}