LoFreq edit Indel quality

lofreq_Indel.xml

<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>