Mercurial > repos > jjohnson > snpeff_with_dep
changeset 5:c641d515de2e
Add stdio tags
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 14 Sep 2012 13:12:02 -0500 |
| parents | ceaa79a5ee16 |
| children | e6b662b96061 |
| files | snpEff.xml snpEff_download.xml snpSift_annotate.xml snpSift_caseControl.xml snpSift_filter.xml snpSift_int.xml |
| diffstat | 6 files changed, 22 insertions(+), 4 deletions(-) [+] |
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--- a/snpEff.xml Fri Sep 14 07:51:23 2012 -0500 +++ b/snpEff.xml Fri Sep 14 13:12:02 2012 -0500 @@ -481,7 +481,10 @@ </data> <data format="html" name="statsFile" /> </outputs> - + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> <help> This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions.
--- a/snpEff_download.xml Fri Sep 14 07:51:23 2012 -0500 +++ b/snpEff_download.xml Fri Sep 14 13:12:02 2012 -0500 @@ -413,6 +413,10 @@ <outputs> <data format="txt" name="logfile" /> </outputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> <help>
--- a/snpSift_annotate.xml Fri Sep 14 07:51:23 2012 -0500 +++ b/snpSift_annotate.xml Fri Sep 14 13:12:02 2012 -0500 @@ -14,7 +14,8 @@ <param format="vcf" name="dbSnp" type="data" label="VCF File with ID field annotated (e.g. dnSNP.vcf)" help="The ID field for a variant in input will be assigned from a matching variant in this file."/> </inputs> <stdio> - <exit_code range="-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> </stdio> <outputs>
--- a/snpSift_caseControl.xml Fri Sep 14 07:51:23 2012 -0500 +++ b/snpSift_caseControl.xml Fri Sep 14 13:12:02 2012 -0500 @@ -28,6 +28,10 @@ <outputs> <data format="vcf" name="output" /> </outputs> + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> <help>
--- a/snpSift_filter.xml Fri Sep 14 07:51:23 2012 -0500 +++ b/snpSift_filter.xml Fri Sep 14 13:12:02 2012 -0500 @@ -26,7 +26,10 @@ <outputs> <data format="vcf" name="output" /> </outputs> - + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> <help> You can filter using arbitrary expressions.
--- a/snpSift_int.xml Fri Sep 14 07:51:23 2012 -0500 +++ b/snpSift_int.xml Fri Sep 14 13:12:02 2012 -0500 @@ -18,7 +18,10 @@ <outputs> <data format="vcf" name="output" /> </outputs> - + <stdio> + <exit_code range=":-1" level="fatal" description="Error: Cannot open file" /> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> <help> You can filter using intervals (BED file)