Mercurial > repos > dave > abayesqr
changeset 0:1b624d47d935 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abayesqr commit dcedcb76831fd639d1468a308a78ac359ecd2496
author | dave |
---|---|
date | Mon, 18 Mar 2019 16:07:22 -0400 |
parents | |
children | 3e9704b9d49e |
files | abayesqr.xml |
diffstat | 1 files changed, 54 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/abayesqr.xml Mon Mar 18 16:07:22 2019 -0400 @@ -0,0 +1,54 @@ +<?xml version="1.0"?> +<tool id="abayesqr" name="aBayesQR" version="1.0.0"> + <description>for haplotype reconstruction</description> + <requirements> + <requirement type="package" version="1.0.0">abayesqr</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$reference' input.fasta && + ln -s '$input' input.sam && + aBayesQR $abayes_params + ]]> + </command> + <configfiles> + <configfile name="abayes_params"><![CDATA[filename of reference sequence (FASTA) : input.fasta +filname of the aligned reads (sam format) : input.sam +paired-end (1 = true, 0 = false) : $paired +SNV_thres : $snv +reconstruction_start : $start +reconstruction_stop: $stop +min_mapping_qual : $qual +min_read_length : $readlength +max_insert_length : $insertlength +characteristic zone name : $zone +seq_err (assumed sequencing error rate(%)) : $seq_err +MEC improvement threshold : $mec_threshold +]]></configfile> + </configfiles> + <inputs> + <param name="input" type="data" format="sam" label="Input reads in SAM format" /> + <param name="reference" type="data" format="fasta" label="Reference genome" /> + <param name="paired" type="boolean" truevalue="1" falsevalue="0" label="Paired reads" /> + <param name="snv" type="float" value="0.01" label="SNV threshold" /> + <param name="start" type="integer" value="1" label="Reconstruction start" /> + <param name="stop" type="integer" value="1300" label="Reconstruction stop" /> + <param name="qual" type="integer" value="60" label="Minimum mapping quality" /> + <param name="readlength" type="integer" value="150" label="Minimum read length" /> + <param name="insertlength" type="integer" value="250" label="Maximum insert length" /> + <param name="zone" type="text" label="Characteristic zone name" /> + <param name="seq_err" type="float" value="0.1" label="Sequencing error rate" /> + <param name="mec_threshold" type="float" value="0.0395" label="MEC improvement threshold" /> + </inputs> + <outputs> + <data name="haplotypes" from_work_dir="haplotypes.fasta" format="fasta" label="${tool.name} on ${on_string} - Haplotypes" /> + </outputs> + <tests> + <test> + </test> + </tests> + <help> + </help> + <citations> + <citation type="doi">10.1089/cmb.2017.0249</citation> + </citations> +</tool>