Mercurial > repos > rchikhi > kmergenie
changeset 7:f7796b819c62 draft
fixed xml
author | Rayan Chikhi <chikhi@psu.edu> |
---|---|
date | Tue, 06 Aug 2013 16:09:45 -0400 |
parents | 3c8d8ebb7d1b |
children | 600357c96710 |
files | kmergenie.xml |
diffstat | 1 files changed, 11 insertions(+), 3 deletions(-) [+] |
line wrap: on
line diff
--- a/kmergenie.xml Tue Aug 06 13:48:34 2013 -0400 +++ b/kmergenie.xml Tue Aug 06 16:09:45 2013 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool id="kmergenie" name="KmerGenie" version="1.5626"> <description>k-mer histograms analysis</description> - <requirements><requirement type="package">kmergenie</requirement></requirements> + <requirements><requirement type="package" version="1.5626">kmergenie</requirement></requirements> <command interpreter="python"> ## assumes that kmergenie folder is in $PATH, my install doesn't use tool_dependency_dir yet stderr_wrapper.py kmergenie $input @@ -12,6 +12,14 @@ #if $params.l != '': -l $params.l #end if + #if $params.s != '': + -s $params.s + #end if + #if $params.sampling_mode.type_select == 'manual': + -e $params.sampling_mode.e + #end if + $params.two_passes + $params.use_diploid #end if -o ${html_file.files_path}/kmergenie_$input.name 1> /dev/null @@ -41,7 +49,7 @@ <when value="autodetect"> </when> </conditional> - <param name="one_pass" type="boolean" label="Precise estimation of k" truevalue="--one-pass" falsevalue="" checked="True" help="Performs a second pass to find the optimal k value within 2 bp" /> + <param name="two_passes" type="boolean" label="Precise estimation of k" truevalue="" falsevalue="--one-pass" checked="True" help="Performs a second pass to find the optimal k value within 2 bp" /> <param name="use_diploid" type="boolean" label="Diploid organism" help="" truevalue="--diploid" falsevalue="" checked="False"/> </when> <when value="autodetect"> @@ -60,7 +68,7 @@ </stdio> <tests> <test> - <param name="input_file" value="1000gsample.fastq" /> + <param name="input" ftype="fastq" value="1000gsample.fastq" /> <param name="type_select" value="autodetect"/> <output name="html_file" file="kmergenie_report.html" ftype="html" lines_diff="1"/> </test>