annotate macros.xml @ 0:6ee7eb5821f0 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/necat commit 6946d81de9419c90e9bc4ea2f7bd5e4168dd6dd6

<?xml version="1.0"?>

<macros>
    <token name="@TOOL_VERSION@">0.0.1_update20200803</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="job_conf">
        <configfile name="job_configfile">
            <![CDATA[
            PROJECT=project
            ONT_READ_LIST=read_list.txt
            GENOME_SIZE=${genome_size}
            THREADS=\${GALAXY_SLOTS:-4}
            
            MIN_READ_LENGTH=${min_read_length}
            PREP_OUTPUT_COVERAGE=${correction_coverage}
             
            OVLP_FAST_OPTIONS=-k ${adv.ovf.k} -z ${adv.ovf.z} -q ${adv.ovf.q} -b ${adv.ovf.b} -n ${adv.ovf.n} -a ${adv.ovf.a} -d ${adv.ovf.d} -e ${adv.ovf.e} -m ${adv.ovf.m} -j 0 -u 1

            OVLP_SENSITIVE_OPTIONS=-k ${adv.ovs.k} -z ${adv.ovs.z} -q ${adv.ovs.q} -b ${adv.ovs.b} -n ${adv.ovs.n} -a ${adv.ovs.a} -d ${adv.ovs.d} -e ${adv.ovs.e} -m ${adv.ovs.m} -j 0 -u 1

            CNS_FAST_OPTIONS=-a ${adv.cnf.a} -x ${adv.cnf.x} -y ${adv.cnf.y} -l ${adv.cnf.l} -e ${adv.cnf.e} -p ${adv.cnf.p} -r ${adv.cnf.r} -u ${adv.cnf.u} 
            
            CNS_SENSITIVE_OPTIONS=-a ${adv.cns.a} -x ${adv.cns.x} -y ${adv.cns.y} -l ${adv.cns.l} -e ${adv.cns.e} -p ${adv.cns.p} -r ${adv.cns.r} -u ${adv.cns.u} 

            TRIM_OVLP_OPTIONS=-n ${adv.tov.n} -a ${adv.tov.a} -z ${adv.tov.z} -b ${adv.tov.b} -e ${adv.tov.e} -j 1 -u 1
                
            ASM_OVLP_OPTIONS=-n ${adv.aov.n} -a ${adv.aov.a} -z ${adv.aov.z} -b ${adv.aov.b} -e ${adv.aov.e} -j 1 -u 0

            NUM_ITER=2
            
            #if $assembly.should_assemble == "yes":
                CNS_OUTPUT_COVERAGE=$assembly.assembly_coverage
                POLISH_CONTIGS=$assembly.polish_contigs
            #else:
                CNS_OUTPUT_COVERAGE=30
                POLISH_CONTIGS=false
            #end if 

            CLEANUP=1
            USE_GRID=false 
            GRID_NODE=0 
            GRID_OPTIONS=
            SMALL_MEMORY=0 
            FSA_OL_FILTER_OPTIONS=
            --min_length={adv.fol.min_length} 
            --max_length={adv.fol.max_length} 
            --min_identity={adv.fol.min_identity}
            --min_aligned_length={adv.fol.min_aligned_length}
            --max_overhang={adv.fol.max_overhang}
            --min_coverage={adv.fol.min_coverage}
            --max_coverage={adv.fol.max_coverage}
            --max_diff_coverage={adv.fol.max_diff_coverage}
            --coverage_discard={adv.fol.coverage_discard}
            --bestn={adv.fol.bestn}
            --genome_size={adv.fol.genome_size}
            --coverage={adv.fol.coverage}
            --thread_size=\${GALAXY_SLOTS:-4}
            --identity_global_deviation1={adv.fol.identity_global_deviation1}
            --identity_global_deviation2={adv.fol.identity_global_deviation2}
            --overhang_global_deviation1={adv.fol.overhang_global_deviation1}
            --overhang_global_deviation2={adv.fol.overhang_global_deviation2}
            --identity_local_deviation1={adv.fol.identity_local_deviation1}
            --identity_local_deviation2={adv.fol.identity_local_deviation2}
            --overhang_local_deviation1={adv.fol.overhang_local_deviation1}
            --overhang_local_deviation2={adv.fol.overhang_local_deviation2}
            --identity_local_condition={adv.fol.identity_local_condition}
            --local_low_coverage={adv.fol.local_low_coverage}
            --overlap_file_type=m4

            FSA_ASSEMBLE_OPTIONS= 
            --min_length={adv.fa.min_length}
            --min_identity={adv.fa.min_identity}
            --min_aligned_length={adv.fa.min_aligned_length}
            --min_contig_length={adv.fa.min_contig_length}
            --max_spur_length={adv.fa.max_spur_length}
            --select_branch={adv.fa.select_branch}
            --overlap_file_type=m4
            --thread_size=\${GALAXY_SLOTS:-4}

            FSA_CTG_BRIDGE_OPTIONS= 
            --read_min_length={adv.fcb.read_min_length}
            --ctg_min_length={adv.fcb.ctg_min_length}
            --ctg2ctg_min_identity={adv.fcb.ctg2ctg_min_identity}
            --ctg2ctg_max_overhang={adv.fcb.ctg2ctg_max_overhang}
            --ctg2ctg_min_aligned_length={adv.fcb.ctg2ctg_min_aligned_length}
            --read2ctg_min_identity={adv.fcb.read2ctg_min_identity}
            --read2ctg_max_overhang={adv.fcb.read2ctg_max_overhang}
            --read2ctg_min_aligned_length={adv.fcb.read2ctg_min_aligned_length}
            --read2ctg_min_coverage={adv.fcb.read2ctg_min_coverage}
            --min_contig_length={adv.fcb.min_contig_length}
            --select_branch={adv.fcb.select_branch}
            --window_size={adv.fcb.window_size}
            --thread_size=\${GALAXY_SLOTS:-4}
            ]]>
        </configfile>
    </xml>



    <xml name="overlap_sensitive_options">
        <section name="ovs" title="Overlap sensitive options (for oc2pmov subprogram)" expanded="false" help="OVLP_SENSITIVE_OPTIONS. Passed to oc2pmov in the first round of error correction.">
            <param argument="-n" type="integer" min="1" max="100000" value="500" label="number of candidates" help="" />
            <param argument="-k" type="integer" min="1" max="100" value="15" label="kmer size" help="" />
            <param argument="-q" type="integer" min="1" max="100000" value="500" label="max kmer occurances" help="" />
            <param argument="-z" type="integer" min="1" max="100" value="10" label="scan window size" help="" />
            <param argument="-b" type="integer" min="1" max="100000" value="2000" label="block size" help="" />
            <param argument="-a" type="integer" min="1" max="100000" value="1000" label="min align length" help="" />
            <param argument="-d" type="float" min="0" max="1" value="0.25" label="ddf score cutoff" help="" />
            <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" />
            <param argument="-m" type="integer" min="1" max="100000" value="500" label="number of output" help="" />
        </section>
    </xml>



    <xml name="consensus_sensitive_options">
        <section name="cns" title="Consensus sensitive options (for oc2cns subprogram)" expanded="false" help="CNS_SENSITIVE_OPTIONS. Passed to oc2cns in the first round of error correction.">
            <param argument="-a" type="integer" min="1" max="100000" value="2000" label="align length cutoff" help="" />
            <param argument="-x" type="integer" min="1" max="10000" value="4" label="minimal coverage" help="" />
            <param argument="-y" type="integer" min="1" max="10000" value="12" label="maximal coverage" help="" />
            <param argument="-l" type="integer" min="1" max="10000000" value="1000" label="minimal length of corrected reads" help="" />
            <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" />
            <param argument="-p" type="float" min="0" max="1" value="0.80" label="minimal mapping ratio" help="" />
            <param argument="-r" type="boolean" truevalue="1" falsevalue="0" label="rescue long indels?" help=""/>
            <param argument="-u" type="boolean" truevalue="1" falsevalue="0" label="use fixed ident cutoff?" help="default (no) is dynamic cutoff."/>
        </section>
    </xml>



    <xml name="overlap_fast_options">
        <section name="ovf" title="Overlap fast options (for oc2pmov subprogram)" expanded="false" help="OVLP_FAST_OPTIONS. Passed to oc2pmov in the second round of error correction.">
            <param argument="-n" type="integer" min="1" max="100000" value="500" label="number of candidates" help="" />
            <param argument="-k" type="integer" min="1" max="100" value="15" label="kmer size" help="" />
            <param argument="-q" type="integer" min="1" max="100000" value="500" label="max kmer occurances" help="" />
            <param argument="-z" type="integer" min="1" max="100" value="20" label="scan window size" help="" />
            <param argument="-b" type="integer" min="1" max="100000" value="2000" label="block size" help="" />
            <param argument="-a" type="integer" min="1" max="100000" value="1000" label="min align length" help="" />
            <param argument="-d" type="float" min="0" max="1" value="0.25" label="ddf score cutoff" help="" />
            <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" />
            <param argument="-m" type="integer" min="1" max="100000" value="500" label="number of outputs" help="" />
        </section>
    </xml>



    <xml name="consensus_fast_options">
        <section name="cnf" title="Consensus fast options (for oc2cns subprogram)" expanded="false" help="CNS_FAST_OPTIONS. Passed to oc2cns in the second round of error correction.">
            <param argument="-a" type="integer" min="1" max="100000" value="400" label="align length cutoff" help="" />
            <param argument="-x" type="integer" min="1" max="10000" value="4" label="minimal coverage" help="" />
            <param argument="-y" type="integer" min="1" max="10000" value="12" label="maximal coverage" help="" />
            <param argument="-l" type="integer" min="1" max="10000000" value="500" label="minimal length of corrected reads" help="" />
            <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" />
            <param argument="-p" type="float" min="0" max="1" value="0.80" label="minimal mapping ratio" help="" />
            <param argument="-r" type="boolean" truevalue="1" falsevalue="0" label="rescue long indels?" help=""/>
            <param argument="-u" type="boolean" truevalue="1" falsevalue="0" label="use fixed ident cutoff?" help="default (no) is dynamic cutoff."/>
        </section>
    </xml>


    <xml name="trimming_overlap_options">
        <section name="tov" title="Trimming overlap options (for oc2asmpm subprogram)" expanded="false" help="TRIM_OVLP_OPTIONS. Passed to oc2asmpm. ">
            <param argument="-n" type="integer" min="1" max="100000" value="100" label="number of candidates" help="" />
            <param argument="-a" type="integer" min="1" max="100000" value="400" label="min align length" help="" />
            <param argument="-z" type="integer" min="1" max="100" value="10" label="scan window size" help="" />
            <param argument="-b" type="integer" min="1" max="100000" value="2000" label="block size" help="" />
            <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" />
        </section>
    </xml>


    <xml name="assembly_overlap_options">
        <section name="aov" title="Assembly Overlap Options (for oc2asmpm subprogram)" expanded="false" help="ASM_OVLP_OPTIONS. Passed to oc2asmpm. ">
            <param argument="-n" type="integer" min="1" max="100000" value="100" label="number of candidates" help="" />
            <param argument="-a" type="integer" min="1" max="100000" value="400" label="min align length" help="" />
            <param argument="-z" type="integer" min="1" max="100" value="10" label="scan window size" help="" />
            <param argument="-b" type="integer" min="1" max="100000" value="2000" label="block size" help="" />
            <param argument="-e" type="float" min="0" max="1" value="0.50" label="sequencing error" help="" />
        </section>
    </xml>


    <xml name="assembly_overlap_filtering">
        <section name="fol" title="Assembly Overlap Filtering Options (for fsa_ol_filter subprogram)" expanded="false" help="Filters out low-quality overlaps for assembly. ">
            <param argument="--min_length" type="integer" min="1" value="2500" label="min read length" help="" />
            <param argument="--max_length" type="integer" min="1" value="2147483647" label="max read length" help="" />
            <param argument="--min_identity" type="float" min="-1" value="-1" label="min identity of overlaps" help="" />
            <param argument="--min_aligned_length" type="integer" min="0"  value="2500" label="min aligned length of overlaps" help="" />
            <param argument="--max_overhang" type="integer" min="-1" value="-1" label="max overhang" help="maximum overhang of overlaps, negative number = determined by the program. default: -1" />
            <param argument="--min_coverage" type="integer" min="-1" value="-1" label="min base coverage. " help="set automatically using '-1'" />
            <param argument="--max_coverage" type="integer" min="-1" value="-1" label="max base coverage. " help="set automatically using '-1'" />
            <param argument="--max_diff_coverage" type="integer" min="-1" value="-1" label="max difference of base coverage. " help="set automatically using '-1'" />
            <param argument="--coverage_discard" type="float" min="0" value="0.01" label="discard ratio of base coverage. If max_coverage or max_diff_coverage is negative, it will be reset to (100-coverage_discard)th percentile" help="" />
            <param argument="--bestn" type="integer" min="1" value="10" label="bestn" help="output best n overlaps on 5' or 3' end for each read." />
            <param argument="--genome_size" type="integer" min="0" value="0" label="genome size" help="Genome size. Determines the maximum length of reads with coverage together" />
            <param argument="--coverage" type="integer" min="0" value="40" label="coverage" help="determines the maximum length of reads with genome_size together" />
            <param argument="--identity_global_deviation1" type="integer" value="98" label="identity global deviation 1" help="If min_identity &#60; 0, min_identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 98" />
            <param argument="--identity_global_deviation2" type="integer" value="6" label="identity global deviation 2" help="If min_identity &#60; 0, min_identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 6" />
            <param argument="--overhang_global_deviation1" type="float" value="30" label="overhang global deviation 1" help="If max_overhang &#60; 0, max_overhang is set to max(m, deviation1) + 1.4826*mad*deviation2 default: 30" />
            <param argument="--overhang_global_deviation2" type="float" value="6" label="overhang global deviation 2" help="If max_overhang &#60; 0, max_overhang is set to max(m, deviation1) + 1.4826*mad*deviation2 default: 6" />
            <param argument="--identity_local_deviation1" type="float" min="0" value="99" label="identity local deviation 1" help="The local threshold of identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 99" />
            <param argument="--identity_local_deviation2" type="float" min="0" value="6" label="identity local deviation 2" help="The local threshold of identity is set to min(m, deviation1) - 1.4826*mad*deviation2 default: 6" />
            <param argument="--overhang_local_deviation1" type="float" min="0" value="10" label="overhang local deviation 1" help="The local threshold of overhang is set to max(m, deviation1) + 1.253*mad*deviation2 default: 10" />
            <param argument="--overhang_local_deviation2" type="float" min="0" value="6" label="overhang local deviation 2" help="The local threshold of overhang is set to max(m, deviation1) + 1.253*mad*deviation2 default: 6" />
            <param argument="--identity_local_condition" type="integer" min="0" max="1" value="0" label="identity local condition" help="Local filtering conditions. 0 = overlap idenitity &#60; threshold, 1 = overlap idenitity &#60; threshold and query identity >= target identity default: 0" />
            <param argument="--local_low_coverage" type="integer" min="0" value="25" label="local low coverage" help="If the coverage of reads is less than local_low_coverage, min_identity and max_overhang are used to filter out low-quality overlaps. Otherwise, the local threshold is used. default: 25" />
        </section>
    </xml>


    <xml name="contig_assembly">
        <section name="fa" title="Contig Assembly Options (for fsa_assemble subprogram)" expanded="false" help="Passed to fsa_assemble subprogram. Constructs contigs from filtered overlaps and corrected reads. ">
            <param argument="--min_length" type="integer" min="0" value="0" label="min read length" help="minimum length of reads" />
            <param argument="--min_identity" type="float" min="0" max="100" value="0" label="min overlap identity" help="minimum identity of overlaps" />
            <param argument="--min_contig_length" type="integer" min="1" value="500" label="min contig length" help="minimum length of contigs" />
            <param argument="--max_spur_length" type="integer" min="1" value="50000" label="max spur length" help="branches less the threshod are treated as spurs" />
            <param argument="--select_branch" type="boolean" truevalue="best" falsevalue="no" label="select branch" help="select the most probable branch. default is no." />
        </section>
    </xml>



    <xml name="contig_bridging">
        <section name="fcb" title="Contig Bridging Options (for fsa_ctg_bridge subprogram)" expanded="false" help="Passed to fsa_ctg_bridge subprogram. Bridges contigs using long reads ">
            <param argument="--read_min_length" type="integer" min="1" value="5000" label="read min length" help="minimum rawread length" />
            <param argument="--ctg_min_length" type="integer" min="1" value="500" label="contig min length" help="minimum contig length" />

            <param argument="--ctg2ctg_min_identity" type="float" min="1" max="100" value="95" label="ctg2ctg_min_identity" help="minimum identity of overlaps between contigs" />
            <param argument="--ctg2ctg_max_overhang" type="integer" min="1" value="100" label="contig-contig max overhang" help="maximum overhang of overlaps between contigs" />
            <param argument="--ctg2ctg_min_aligned_length" type="integer" min="1" value="2000" label="contig-contig min aligned length" help="minimum aligned length of overlaps between contigs" />

            <param argument="--read2ctg_min_identity" type="float" min="1" max="100" value="80" label="read-contig min identity" help="minimum identity of overlaps between rawreads and contigs" />
            <param argument="--read2ctg_max_overhang" type="integer" min="1" value="500" label="read-contig max overhang" help="maximum overhang of overlaps between rawreads and contigs" />
            <param argument="--read2ctg_min_aligned_length" type="integer" min="1" value="5000" label="read-contig min aligned length" help="minimum aligned length of overlaps between rawreads and contigs" />
            <param argument="--read2ctg_min_coverage" type="integer" min="1" value="3" label="read-contig min coverage" help="minimum coverage of links between rawreads and contigs" />

            <param argument="--min_contig_length" type="integer" min="1" value="500" label="min contig length" help="minimum length of bridged contigs" />
            <param argument="--window_size" type="integer" min="1" value="1000" label="window size" help="threshold is used to group rawreads that bridge contigs" />
            <param argument="--select_branch" type="boolean" truevalue="best" falsevalue="no" label="select branch" help="select the most probable branch. default is no." />
        </section>
    </xml>



    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41467-020-20236-7</citation>
        </citations>
    </xml>
</macros>