Mercurial > repos > iuc > qualimap_bamqc
changeset 3:5f8e69cc4c6e draft
"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 | e7fd6754d093 |
| children | 19ece8afbaab |
| files | qualimap_bamqc.xml |
| diffstat | 1 files changed, 6 insertions(+), 2 deletions(-) [+] |
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--- a/qualimap_bamqc.xml Mon Jan 13 13:04:33 2020 -0500 +++ b/qualimap_bamqc.xml Sat May 16 09:47:55 2020 -0400 @@ -1,4 +1,4 @@ -<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy1"> +<tool id="qualimap_bamqc" name="QualiMap BamQC" version="@VERSION@+galaxy2"> <macros> <import>qualimap_macros.xml</import> </macros> @@ -6,6 +6,7 @@ <expand macro="version_command" /> <command detect_errors="exit_code"><![CDATA[ #import os + #import re @SET_JAVA_OPTS@ && ## Set some default file names and paths @@ -39,8 +40,11 @@ #end if #end if + #set input_name = re.sub('[^\s\w\-]', '_', str($input1.name)) + ln -s '$input1' '$input_name' && + qualimap bamqc - -bam '$input1' -outdir results -outformat html + -bam '$input_name' -outdir results -outformat html --collect-overlap-pairs #if str($stats_regions.region_select) == 'custom_regions': -gff ${regions_file} ${stats_regions.outside_stats}