comparison bbmap.xml @ 13:456d8ebb6a28 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb

12:3f94a2e3d513

                <option value="lr">Trim both</option>
            </param>
            <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/>
            <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
            <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
            <param argument="fakefastaquality" type="integer" value="-1" max="50" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
            <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/>
            <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
            <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/>
            <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/>
        </section>

                <option value="name">Sort by read names</option>
                <option value="unsorted">Not sorted (sorted as input)</option>
            </param>
        </section>
        <section name="pf_options" title="Post-filtering options">
            <param argument="idfilter" type="integer" value="0" min="0" max="1" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
            <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/>
            <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/>
            <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/>
            <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/>
            <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/>

    * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file.

    </help>
    <expand macro="citations"/>
</tool>

13:456d8ebb6a28

                <option value="lr">Trim both</option>
            </param>
            <param argument="untrim" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Undo trimming after mapping?" help="Untrimmed bases will be soft-clipped in cigar strings"/>
            <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
            <param argument="mintrimlength" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
            <param argument="fakefastaquality" type="integer" max="50" value="-1" label="Set to a positive number 1-50 to generate fake quality strings for fasta input reads"/>
            <param argument="ignorebadquality" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Keep going, rather than crashing, if a read has out-of-range quality values?"/>
            <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
            <param argument="minaveragequality" type="integer" value="0" label="Do not map reads with average quality below this value"/>
            <param argument="maqb" type="integer" value="0" label="Calculate maq from this many initial bases" help="Zero value ignores"/>
        </section>

                <option value="name">Sort by read names</option>
                <option value="unsorted">Not sorted (sorted as input)</option>
            </param>
        </section>
        <section name="pf_options" title="Post-filtering options">
            <param argument="idfilter" type="integer" min="0" max="1" value="0" label="Specify exact minimum identity allowed for alignments to be output" help="Independent of approximate minimum alignment identity to look for"/>
            <param argument="subfilter" type="integer" value="-1" label="Ban alignments with more than this many substitutions" help="Negative value ignores"/>
            <param argument="insfilter" type="integer" value="-1" label="Ban alignments with more than this many insertions" help="Negative value ignores"/>
            <param argument="delfilter" type="integer" value="-1" label="Ban alignments with more than this many deletions" help="Negative value ignores"/>
            <param argument="indelfilter" type="integer" value="-1" label="Ban alignments with more than this many indels" help="Negative value ignores"/>
            <param argument="editfilter" type="integer" value="-1" label="Ban alignments with more than this many edits" help="Negative value ignores"/>

    * Not sorted (sorted as input) - the file is sorted in the order of the reads in the input file.

    </help>
    <expand macro="citations"/>
</tool>