Mercurial > repos > iuc > sra_tools
changeset 4:62e4d56ebb6f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4091428e9e28ca06263bc00cdf938d20f620aa4d
| author | iuc |
|---|---|
| date | Fri, 21 Oct 2016 04:32:19 -0400 |
| parents | 4732693f4661 |
| children | 26b7446bb17e |
| files | fastq_dump.xml sam_dump.xml sra_macros.xml sra_pileup.xml |
| diffstat | 4 files changed, 4 insertions(+), 7 deletions(-) [+] |
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--- a/fastq_dump.xml Tue Oct 18 14:54:40 2016 -0400 +++ b/fastq_dump.xml Fri Oct 21 04:32:19 2016 -0400 @@ -4,11 +4,8 @@ <import>sra_macros.xml</import> </macros> <expand macro="requirements"/> - <stdio> - <exit_code range="127" level="fatal" description="Could not locate fastq-dump binary"/> - </stdio> <version_command>fastq-dump --version</version_command> - <command> + <command detect_errors="exit_code"> <![CDATA[ #if $input.input_select=="file_list":
--- a/sam_dump.xml Tue Oct 18 14:54:40 2016 -0400 +++ b/sam_dump.xml Fri Oct 21 04:32:19 2016 -0400 @@ -5,7 +5,7 @@ </macros> <expand macro="requirements"/> <version_command>sam-dump --version</version_command> - <command> + <command detect_errors="exit_code"> <![CDATA[ #if $input.input_select=="file_list": for acc in `cat $input.file_list` ;
--- a/sra_macros.xml Tue Oct 18 14:54:40 2016 -0400 +++ b/sra_macros.xml Fri Oct 21 04:32:19 2016 -0400 @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">2.7.0</token> + <token name="@VERSION@">2.7.0.1</token> <macro name="requirements"> <requirements> <requirement type="package" version="2.7.0">sra-tools</requirement>
--- a/sra_pileup.xml Tue Oct 18 14:54:40 2016 -0400 +++ b/sra_pileup.xml Fri Oct 21 04:32:19 2016 -0400 @@ -5,7 +5,7 @@ </macros> <expand macro="requirements"/> <version_command>sra-pileup --version</version_command> - <command> + <command detect_errors="exit_code"> <![CDATA[ ## Need to set the home directory to the current working directory, ## else the tool tries to write to home/.ncbi and fails when used