Mercurial > repos > stheil > metavelvet_wrapper
diff velvet_macro.xml @ 2:1bb80c25b379 draft
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| author | stheil |
|---|---|
| date | Thu, 24 Sep 2015 10:42:44 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/velvet_macro.xml Thu Sep 24 10:42:44 2015 -0400 @@ -0,0 +1,147 @@ +<macros> + + <xml name="paired_library_options"> + <param name="ins_length" type="integer" optional="true" label="Expected distance between two paired end reads"/> + <param name="ins_length_sd" type="integer" optional="true" label="Standard deviation for paired end reads length (default: 10% of corresponding length)"/> + <repeat min="1" name="files" title="Input files"> + <conditional name="fileFormat"> + <param name="format" type="select" label="File format"> + <option value="-fasta">fasta</option> + <option value="-fastq">fastq</option> + <option value="-fasta_gz">fasta.gz</option> + <option value="-fastq_gz">fastq.gz</option> + </param> + <when value="-fasta"> + <conditional name="fileLayout"> + <param name="layout" type="select" label="File layout"> + <option value="-interleaved">interleaved</option> + <option value="-separate">separate</option> + </param> + <when value="-interleaved"> + <param name="sequence" type="data" format="fasta" label="Interleaved sequence file"/> + </when> + <when value="-separate"> + <param name="sequence" type="data" format="fasta" label="Forward sequence file"/> + <param name="sequencePair" type="data" format="fasta" optional="true" label="Reverse sequence file"/> + </when> + </conditional> + </when> + <when value="-fasta_gz"> + <conditional name="fileLayout"> + <param name="layout" type="select" label="File layout"> + <option value="-interleaved">interleaved</option> + <option value="-separate">separate</option> + </param> + <when value="-interleaved"> + <param name="sequence" type="data" format="fasta.gz" label="Interleaved sequence file"/> + </when> + <when value="-separate"> + <param name="sequence" type="data" format="fasta.gz" label="Forward sequence file"/> + <param name="sequencePair" type="data" format="fasta.gz" optional="true" label="Reverse sequence file"/> + </when> + </conditional> + </when> + <when value="-fastq"> + <conditional name="fileLayout"> + <param name="layout" type="select" label="File layout"> + <option value="-interleaved">interleaved</option> + <option value="-separate">separate</option> + </param> + <when value="-interleaved"> + <param name="sequence" type="data" format="fastq" label="Interleaved sequence file"/> + </when> + <when value="-separate"> + <param name="sequence" type="data" format="fastq" label="Forward sequence file"/> + <param name="sequencePair" type="data" format="fastq" optional="true" label="Reverse sequence file"/> + </when> + </conditional> + </when> + <when value="-fastq_gz"> + <conditional name="fileLayout"> + <param name="layout" type="select" label="File layout"> + <option value="-interleaved">interleaved</option> + <option value="-separate">separate</option> + </param> + <when value="-interleaved"> + <param name="sequence" type="data" format="fastq.gz" label="Interleaved sequence file"/> + </when> + <when value="-separate"> + <param name="sequence" type="data" format="fastq.gz" label="Forward sequence file"/> + <param name="sequencePair" type="data" format="fastq.gz" optional="true" label="Reverse sequence file"/> + </when> + </conditional> + </when> + </conditional> + </repeat> + </xml> + + <token name="@PAIRED_FILES_OPTIONS@"> + + #for $j, $file in enumerate( $library.files ) + + $file.fileFormat.format + + #if $file.fileFormat.fileLayout.layout == "-separate" + -separate $file.fileFormat.fileLayout.sequence $file.fileFormat.fileLayout.sequencePair + #else + -interleaved $file.fileFormat.fileLayout.sequence + #end if + + #end for + + </token> + + <xml name="unpaired_library_options"> + <repeat min="1" name="files" title="Input files"> + <conditional name="fileFormat"> + <param name="format" type="select" label="File format"> + <option value="-fasta">fasta</option> + <option value="-fastq">fastq</option> + <option value="-raw">raw</option> + <option value="-fasta_gz">fasta.gz</option> + <option value="-fastq_gz">fastq.gz</option> + <option value="-raw_gz">raw.gz</option> + <option value="-sam">sam</option> + <option value="-bam">bam</option> + </param> + <when value="-fasta"> + <param name="sequence" type="data" format="fasta" label="Sequence file"/> + </when> + <when value="-fasta_gz"> + <param name="sequence" type="data" format="fasta.gz" label="Sequence file"/> + </when> + <when value="-fastq"> + <param name="sequence" type="data" format="fastq" label="Sequence file"/> + </when> + <when value="-fastq_gz"> + <param name="sequence" type="data" format="fastq.gz" label="Sequence file"/> + </when> + <when value="-raw"> + <param name="sequence" type="data" format="txt" label="Sequence file"/> + </when> + <when value="-raw_gz"> + <param name="sequence" type="data" format="txt" label="Sequence file"/> + </when> + <when value="-sam"> + <param name="sequence" type="data" format="sam" label="Sequence file"/> + </when> + <when value="-bam"> + <param name="sequence" type="data" format="bam" label="Sequence file"/> + </when> + </conditional> + </repeat> + </xml> + + <token name="@UNPAIRED_FILES_OPTIONS@"> + + #for $j, $file in enumerate( $library.files ) + + $file.fileFormat.format + + $file.fileFormat.sequence + + #end for + + </token> + +</macros>