| Previous changeset 2:e7fd6754d093 (2020-01-13) Next changeset 4:19ece8afbaab (2020-05-20) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qualimap commit bd94f00ad5d023ae392ca8fc2378fd5a78bed875" |
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modified:
qualimap_bamqc.xml |
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| diff -r e7fd6754d093 -r 5f8e69cc4c6e qualimap_bamqc.xml --- 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} |