Mercurial > repos > iuc > lofreq_indelqual
diff lofreq_indelqual.xml @ 0:5d6a078d30b0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 9efcb813ab17041c7f5aad834dfff45bd7046c60"
author | iuc |
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date | Tue, 17 Dec 2019 17:26:54 -0500 |
parents | |
children | 354b534eeab7 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lofreq_indelqual.xml Tue Dec 17 17:26:54 2019 -0500 @@ -0,0 +1,78 @@ +<tool id="lofreq_indelqual" name="Insert indel qualities" version="@WRAPPER_VERSION@0"> + <description>into a BAM file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + #if $strategy.selector == 'dindel' + #set $reference_source = $strategy.reference_source + @PREPARE_REF@ + #end if + lofreq indelqual + #if $strategy.selector == 'dindel' + --dindel + --ref $reference_fasta_fn + #else + #if $strategy.deletions + --uniform $strategy.insertions,$strategy.deletions + #else + --uniform $strategy.insertions + #end if + #end if + -o output.bam $reads + ]]></command> + <inputs> + <param type="data" name="reads" format="bam" label="Reads" /> + <conditional name="strategy"> + <param name="selector" type="select" label="Indel calculation approach"> + <option value="uniform">Uniform</option> + <option value="dindel">Dindel</option> + </param> + <when value="uniform"> + <param name="insertions" type="integer" value="30" label="Indel quality to add" help="Should probably not be left at the default value" /> + <param name="deletions" type="integer" optional="true" label="Separate deletion quality" help="Leave blank to use the same values for insertions and deletions" /> + </when> + <when value="dindel"> + <expand macro="reference_interface" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="output" format="bam" from_work_dir="output.bam" label="Add indel qualities to data ${reads.dataset.hid}" /> + </outputs> + <tests> + <test> + <param name="reads" ftype="bam" value="lofreq-in1.bam" /> + <param name="selector" value="uniform" /> + <param name="insertions" value="20" /> + <param name="deletions" value="30" /> + <output name="output" file="indelqual-out1.bam" /> + </test> + <test> + <param name="reads" ftype="bam" value="lofreq-in1.bam" /> + <param name="selector" value="dindel" /> + <param name="ref_selector" value="history" /> + <param name="ref" ftype="fasta" value="pBR322.fa" /> + <output name="output" file="indelqual-out2.bam" /> + </test> + <test> + <param name="reads" ftype="bam" value="lofreq-in1.bam" /> + <param name="selector" value="uniform" /> + <param name="insertions" value="20" /> + <output name="output" file="indelqual-out3.bam" /> + </test> + </tests> + <help><![CDATA[ +Insert indel qualities into BAM file + +The tool has two modes: 'uniform' and 'dindel': + - 'uniform' will assign a given value uniformly, whereas + - 'dindel' will insert indel qualities based on Dindel. + +Both will overwrite any existing values. Do not realign your BAM file afterwards! + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1101/gr.112326.110</citation> + </expand> +</tool>