comparison pilon.xml @ 1:11e5408fd238 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pilon commit f11cbbf24637c96c53e4a1ea5ace4b21e116677c

0:fe0dc27e6327

<tool id="pilon" name="pilon" version="0.1">
    <description>An automated genome assembly improvement and variant detection tool</description>
    <requirements>
      <requirement type="package" version="1.18">pilon</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if $auto_selection.auto_enabled == "yes"
        #for $bamfile in $auto_selection.bam
          ln -f -s "$bamfile" "\$(basename $bamfile)" &&

          --chunksize $options.chunk_size
          $options.diploid
          $options.duplicates
          $options.iupac
          $options.nonpf
          #if len($options.targetlist.strip()) > 0
            --targetlist $options.targetlist
          #end if
          --fix $options.fixes
          $options.verbose
          --defaultqual $options.defaultqual
          --flank $options.flank

        <param label="Source for reference genome used for BAM alignments" name="reference_genome_source" type="select">
          <option selected="True" value="history">Use a genome from history</option>
          <option value="builtin">Use a built-in genome"</option>
        </param>
        <when value="history">
          <param format="fasta" type="data" metadata_name="dbkey" name="history_item" />
        </when>
        <when value="builtin">
          <param label="Select a reference genome" name="builtin" type="select">
            <options from_data_table="all_fasta">
              <filter column="2" type="sort_by" />

            <option value="local">Detect and fix local misassemblies</option>
            <option value="none">Do none of these fixes (no FASTA will be written)</option>
            <option value="amb">Fix ambigious bases in FASTA output (experimental)</option>
            <option value="breaks">Allow local reassembly to open new gaps (experimental, requires local assembly fixing to be selected)</option>
            <option value="novel">Assemble novel sequence from unaligned non-jump reads (experimental)</option>
          </param>
          <param argument="diploid" label="Organism is diploid" type="boolean" checked="false"
            help="Sample is from diploid organism; will eventually affect calling of heterozygous SNPs"
            truevalue="--diploid" falsevalue="" />
          <param argument="duplicates" label="Use duplicates" type="boolean" checked="false"

            help="Output IUPAC ambiguous base codes in the output FASTA file when appropriate"
            truevalue="--iupac" falsevalue="" />
          <param argument="nonpf" label="Use low quality reads" type="boolean" checked="false"
            help="Use reads which failed sequencer quality filtering"
            truevalue="--nonpf" falsevalue="" />
          <param argument="targetlist" label="List of targets to process (leave blank for all)" default="" type="text" length="40"
            help="Only process the specified target(s).  Targets are comma-separated, and each target is a fasta element name optionally followed by a base range." />
          <param argument="verbose" label="Verbose output (in tool log)" type="boolean" check="false"
            truevalue="--verbose" falsevalue="" />
          <param argument="defaultqual" label="Default base quality" type="integer" min="1" value="15"
            help="Assumes bases are of this quality if quals are no present in input BAMs" />
          <param argument="flank" label="Flanking bases to ignore" type="integer" min="1" value="10"
            help="This many bases at each end of the good reads will be ignored." />

1:11e5408fd238

<tool id="pilon" name="pilon" version="1.20.1">
    <description>An automated genome assembly improvement and variant detection tool</description>
    <requirements>
      <requirement type="package" version="1.20">pilon</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
      #if $auto_selection.auto_enabled == "yes"
        #for $bamfile in $auto_selection.bam
          ln -f -s "$bamfile" "\$(basename $bamfile)" &&

          --chunksize $options.chunk_size
          $options.diploid
          $options.duplicates
          $options.iupac
          $options.nonpf
          #if len($options.targets.strip()) > 0
            --targets $options.targets
          #end if
          --fix $options.fixes
          $options.verbose
          --defaultqual $options.defaultqual
          --flank $options.flank

        <param label="Source for reference genome used for BAM alignments" name="reference_genome_source" type="select">
          <option selected="True" value="history">Use a genome from history</option>
          <option value="builtin">Use a built-in genome"</option>
        </param>
        <when value="history">
          <param format="fasta" type="data" name="history_item" label="Select a reference genome"/>
        </when>
        <when value="builtin">
          <param label="Select a reference genome" name="builtin" type="select">
            <options from_data_table="all_fasta">
              <filter column="2" type="sort_by" />

            <option value="local">Detect and fix local misassemblies</option>
            <option value="none">Do none of these fixes (no FASTA will be written)</option>
            <option value="amb">Fix ambigious bases in FASTA output (experimental)</option>
            <option value="breaks">Allow local reassembly to open new gaps (experimental, requires local assembly fixing to be selected)</option>
            <option value="novel">Assemble novel sequence from unaligned non-jump reads (experimental)</option>
            <!-- TODO: enable this when documented in pilon <option value="circle">Trim long reads for circular continuity(experimental, requires unpaired reads)</option>-->
          </param>
          <param argument="diploid" label="Organism is diploid" type="boolean" checked="false"
            help="Sample is from diploid organism; will eventually affect calling of heterozygous SNPs"
            truevalue="--diploid" falsevalue="" />
          <param argument="duplicates" label="Use duplicates" type="boolean" checked="false"

            help="Output IUPAC ambiguous base codes in the output FASTA file when appropriate"
            truevalue="--iupac" falsevalue="" />
          <param argument="nonpf" label="Use low quality reads" type="boolean" checked="false"
            help="Use reads which failed sequencer quality filtering"
            truevalue="--nonpf" falsevalue="" />
          <param argument="targets" label="List of targets to process (leave blank for all)" type="text"
            help="Only process the specified target(s).  Targets are comma-separated, and each target is a fasta element name optionally followed by a base range." />
          <param argument="verbose" label="Verbose output (in tool log)" type="boolean" checked="false"
            truevalue="--verbose" falsevalue="" />
          <param argument="defaultqual" label="Default base quality" type="integer" min="1" value="15"
            help="Assumes bases are of this quality if quals are no present in input BAMs" />
          <param argument="flank" label="Flanking bases to ignore" type="integer" min="1" value="10"
            help="This many bases at each end of the good reads will be ignored." />