# HG changeset patch
# User iuc
# Date 1632216831 0
# Node ID 8da515fbc1bfbc0e7b214581c9be3b9fb26b89ae
# Parent fa7ad9b89f4ad075ee4ab6943cac2371245c3832
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit a18f79e7cfe15fd6e1a5f70533616c379e4e7c6a"
diff -r fa7ad9b89f4a -r 8da515fbc1bf macros.xml
--- a/macros.xml Mon Sep 03 13:10:02 2018 -0400
+++ b/macros.xml Tue Sep 21 09:33:51 2021 +0000
@@ -7,6 +7,23 @@
1.9#set $flags = sum(map(int, str($filter).split(',')))
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+ ^[^\s'\":]+(:\d+(-\d+){0,1}){0,1}$
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@@ -83,21 +169,4 @@
-
------
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-.. class:: warningmark
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-**No options available? How to re-detect metadata**
-
-If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps:
-
-1. Click on the **pencil** icon adjacent to the dataset in the history
-2. A new menu will appear in the center pane of the interface
-3. Click **Datatype** tab
-4. Set **New Type** to **BAM**
-5. Click **Save**
-
-The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down.
-
diff -r fa7ad9b89f4a -r 8da515fbc1bf samtools_mpileup.xml
--- a/samtools_mpileup.xml Mon Sep 03 13:10:02 2018 -0400
+++ b/samtools_mpileup.xml Tue Sep 21 09:33:51 2021 +0000
@@ -12,16 +12,15 @@
@PREPARE_IDX_MULTIPLE@
#if $reference_source.reference_source_selector == "history":
- ln -s '${reference_source.ref_file}' &&
- samtools faidx `basename '${reference_source.ref_file}'` &&
+ #set ref_fa = 'ref.fa'
+ ln -s '${reference_source.ref_file}' 'ref.fa' &&
+ samtools faidx ref.fa &&
+ #else:
+ #set ref_fa = str( $reference_source.ref_file.fields.path )
#end if
samtools mpileup
- #if $reference_source.reference_source_selector != "history":
- -f '${reference_source.ref_file.fields.path}'
- #else:
- -f '${reference_source.ref_file}'
- #end if
+ -f '$ref_fa'
#for $i in range(len( $input_bams )):
'${i}'
#end for