Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/make.fastq.xml @ 35:95d75b35e4d2
Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author | certain cat |
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date | Fri, 31 Oct 2014 15:09:32 -0400 |
parents | 49058b1f8d3f |
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<tool id="mothur_make_fastq" name="Make.fastq" version="1.20.0"> <description>Convert fasta and quality to fastq</description> <command interpreter="python"> mothur_wrapper.py --cmd='make.fastq' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.fastq$:'$fastq --outputdir='$logfile.extra_files_path' --fasta=$fasta --qfile=$qfile #if $chooseformat.use: --format=$chooseformat.format #end if </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Fasta Sequence file"/> <param name="qfile" type="data" format="qual" label="qfile - Sequence Quality file"/> <conditional name = "chooseformat"> <param name = "use" type ="boolean" truevalue ="yes" falsevalue="no" label="choose what format your sequences are"/> <when value = "yes"> <param name = "format" type = "select" optional = "true" multiple = "true"> <option value = "sanger" selected="true">sanger</option> <option value = "solexa">solexa</option> <option value = "illumina">illumina</option> <option value = "illumina">illumina1.8+</option> </param> </when> <when value = "no"/> </conditional> </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"> <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="package" version="1.33">mothur</requirement> </requirements> <tests> </tests> <help> **Mothur Overview** Mothur_, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan, provides bioinformatics for the microbial ecology community. .. _Mothur: http://www.mothur.org/wiki/Main_Page **Command Documenation** The fastq.info_ command reads a fasta file and quality file and creates a fastq. .. _fastq.info: http://www.mothur.org/wiki/Make.fastq </help> </tool>