Mercurial > repos > jjohnson > mothur_toolsuite
changeset 14:ee59e5cff3ba
Mothur - make.fastq fix command name and change_format on output fastq according to qual input, fastq.info outputs qual454
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 05 Oct 2011 10:37:11 -0500 |
| parents | 4f797d3eee3a |
| children | a6189f58fedb |
| files | mothur/tools/mothur/make.fastq.xml |
| diffstat | 1 files changed, 9 insertions(+), 2 deletions(-) [+] |
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--- a/mothur/tools/mothur/make.fastq.xml Wed Oct 05 10:34:44 2011 -0500 +++ b/mothur/tools/mothur/make.fastq.xml Wed Oct 05 10:37:11 2011 -0500 @@ -2,7 +2,7 @@ <description>Convert fasta and quality to fastq</description> <command interpreter="python"> mothur_wrapper.py - --cmd='fastq.info' + --cmd='make.fastq' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq --outputdir='$logfile.extra_files_path' --fasta=$fasta @@ -14,7 +14,14 @@ </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> - <data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq"/> + <data format="fastq" name="fastq" label="${tool.name} on ${on_string}: fastq"> + <change_format> + <when input="qfile.ext" value="qual454" format="fastqsanger"/> + <when input="qfile.ext" value="qualillumina" format="fastqillumina"/> + <when input="qfile.ext" value="qualsolexa" format="fastqsolexa"/> + <when input="qfile.ext" value="qualsolid" format="fastqcssanger"/> + </change_format> + </data> </outputs> <requirements> <requirement type="binary">mothur</requirement>