Mercurial > repos > cmonjeau > stacks
changeset 2:c9e10e0d6c10
fix discard file
| author | cmonjeau |
|---|---|
| date | Mon, 24 Aug 2015 15:39:12 +0000 |
| parents | ccfa8e539bdf |
| children | 0e0ff9e9c761 |
| files | STACKS_procrad.py STACKS_procrad.xml tool_dependencies.xml |
| diffstat | 3 files changed, 2 insertions(+), 3 deletions(-) [+] |
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--- a/STACKS_procrad.py Mon Aug 24 10:09:14 2015 +0000 +++ b/STACKS_procrad.py Mon Aug 24 15:39:12 2015 +0000 @@ -36,6 +36,7 @@ parser.add_argument('--outype') parser.add_argument('--qualitenc') parser.add_argument('-D', action='store_true') + parser.add_argument('--discard_file') parser.add_argument('-t') parser.add_argument('-q', action='store_true') parser.add_argument('--activate_advanced_options')
--- a/STACKS_procrad.xml Mon Aug 24 10:09:14 2015 +0000 +++ b/STACKS_procrad.xml Mon Aug 24 15:39:12 2015 +0000 @@ -53,6 +53,7 @@ --qualitenc $options_quality.qualitenc #if $capture: -D + --discard_file $discard_file #end if --activate_advanced_options $activate_advanced_options -t $options_advanced.truncate @@ -244,8 +245,6 @@ <data format="fastq" name="discard_file" label="discard.fastq with ${tool.name} on ${on_string}: demultiplexed and cleaned reads "> <filter>capture</filter> </data> - - </outputs> <stdio>
--- a/tool_dependencies.xml Mon Aug 24 10:09:14 2015 +0000 +++ b/tool_dependencies.xml Mon Aug 24 15:39:12 2015 +0000 @@ -10,4 +10,3 @@ <repository name="package_velvet_1_2_10" changeset_revision="1c500c3e7fdf" owner="rjullien" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu/" /> </package> </tool_dependency> -