Mercurial > repos > zzhou > bamedit
changeset 62:4ebe0aa42cf0 draft
Uploaded
| author | zzhou |
|---|---|
| date | Mon, 26 Nov 2012 14:27:02 -0500 |
| parents | ad92d59fb5e2 |
| children | fdad5f2a7ad9 |
| files | bamedit.xml |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/bamedit.xml Mon Nov 26 14:26:55 2012 -0500 +++ b/bamedit.xml Mon Nov 26 14:27:02 2012 -0500 @@ -9,7 +9,7 @@ <requirement type="package" version="0.1.12">samtools</requirement> </requirements> <description>Merging, splitting, filtering, and QC of BAM files</description> - <command interpreter="python">bamedit.py $options_file str(\$SCRIPT_PATH)</command> + <command interpreter="python">bamedit.py $options_file '\SCRIPT_PATH'</command> <inputs> <conditional name="input_type"> <param name="input_type_selector" type="select" label="Select your BAM command"> @@ -74,7 +74,7 @@ #end if #end if #if str($input_type.input_type_selector) == 'split': -#set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1) } +#set $__options = { 'action':str("split"), 'bamout':str($bamouts1), 'bamout2':str($bamouts2), 'input1':str($input1), 'testing':str('\$SCRIPT_PATH') } #end if #if str($input_type.input_type_selector) == 'filter': #set $__options = { 'action':str("filter"), 'bamout':str($bamoutf), 'input1':str($input1), 'quality':int($input_type.quality) }