| Previous changeset 20:4f774c1e6049 (2018-02-01) Next changeset 22:01ac0a5fedc3 (2019-05-08) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bwa commit 9bbf35d7f47e5ab6b78248c9907b71446d4e7b0c |
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modified:
bwa-mem.xml bwa.xml bwa_macros.xml |
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| diff -r 4f774c1e6049 -r 8d2a528a9513 bwa-mem.xml --- a/bwa-mem.xml Thu Feb 01 12:35:35 2018 -0500 +++ b/bwa-mem.xml Tue Apr 10 18:41:16 2018 -0400 |
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| @@ -8,6 +8,7 @@ <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ +@pipefail@ @set_reference_fasta_filename@ ## Begin BWA-MEM command line |
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| diff -r 4f774c1e6049 -r 8d2a528a9513 bwa.xml --- a/bwa.xml Thu Feb 01 12:35:35 2018 -0500 +++ b/bwa.xml Tue Apr 10 18:41:16 2018 -0400 |
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| @@ -78,6 +78,7 @@ <expand macro="stdio"/> <command> <![CDATA[ +@pipefail@ @set_reference_fasta_filename@ ## setup vars for rg handling... |
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| diff -r 4f774c1e6049 -r 8d2a528a9513 bwa_macros.xml --- a/bwa_macros.xml Thu Feb 01 12:35:35 2018 -0500 +++ b/bwa_macros.xml Tue Apr 10 18:41:16 2018 -0400 |
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| @@ -3,6 +3,8 @@ <token name="@VERSION@">0.7.17</token> + <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token> + <token name="@set_rg_string@"> #set $rg_string = "@RG\\tID:" + str($rg_id) #set $rg_string += $format_read_group("\\tSM:", $rg_sm) |