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LoFreq edit Indel quality
<tool version="0.1.0" name="LoFreq edit Indel quality" id="lofreq_Indel">
<requirements>
<requirement version="2.1.3.1" type="package">lofreq</requirement>
</requirements>
<stdio>
<exit_code range="1:" />
</stdio>
<command detect_errors="exit_code">
<![CDATA[ lofreq indelqual --dindel --ref "$input1" "$input2" --out "$output1" ]]>
</command>
<inputs>
<param name="input1" type="data" format="fasta" label="Indexed reference fasta file"/>
<param name="input2" type="data" format="bam" label="Input Bam File"/>
</inputs>
<outputs>
<data name="output1" format="bam"/>
</outputs>
<tests>
<test>
<param name="input1" value="Typepol_mapping_REF.fasta.fasta"/>
<param name="input2" value="18-11_S19_L001__001.fastq.bam"/>
<output name="output1" file="18-11_processed.bam"/>
</test>
</tests>
<help>
<![CDATA[ FATAL: Need exactly one BAM file as last argument lofreq indelqual: Insert indel qualities into BAM file (required for indel predictions) Usage: lofreq indelqual [options] in.bam Options: -u | --uniform INT[,INT] Add this indel quality uniformly to all bases. Use two comma separated values to specify insertion and deletion quality separately. (clashes with --dindel) --dindel Add Dindel's indel qualities (Illumina specific) (clashes with -u; needs --ref) -f | --ref Reference sequence used for mapping (Only required for --dindel) -o | --out FILE Output BAM file [- = stdout = default] --verbose Be verbose The preferred way of inserting indel qualities should be via GATK's BQSR (>=2) If that's not possible, use this subcommand. The command has two modes: 'uniform' and 'dindel': - 'uniform' will assign a given value uniformly, whereas - 'dindel' will insert indel qualities based on Dindel (PMID 20980555). Both will overwrite any existing values. Do not realign your BAM file afterwards! ]]>
</help>
<citations>
<citation type="bibtex"> @misc{renameTODO, author = {LastTODO, FirstTODO}, year = {TODO}, title = {TODO}, url = {http://csb5.github.io/lofreq/commands/}, }</citation>
</citations>
</tool>
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