comparison maker.xml @ 4:5e96efe6e6c6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/maker commit 91ce5717f05aa1b7dd111d299275f5cdcf6e717b"

3:96ac930d84fa

<?xml version="1.0"?>
<tool id="maker" name="Maker" profile="16.04" version="@VERSION@">
    <description>genome annotation pipeline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)

#else if $repeat_masking.repeat_source.source_type == 'library'
model_org= # select a model organism for RepBase masking in RepeatMasker
rmlib=${repeat_masking.repeat_source.repeatmasker.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker

#if $repeat_masking.repeat_source.repeat_protein
repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner
#else
repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner

                  </when>
                </conditional>
                <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
              </when>
              <when value="library">
                <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" />
                <param name="rm_gff" type="data" format="fasta" label="Pre-identified repeat elements from an external GFF file" optional="True" />
                <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
              </when>
              <when value="no"/>
            </conditional>
        </section>

4:5e96efe6e6c6

<?xml version="1.0"?>
<tool id="maker" name="Maker" profile="16.04" version="@VERSION@+galaxy1">
    <description>genome annotation pipeline</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
softmask=${repeat_masking.repeat_source.softmask} # use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)

#else if $repeat_masking.repeat_source.source_type == 'library'
model_org= # select a model organism for RepBase masking in RepeatMasker
#if $repeat_masking.repeat_source.rmlib
rmlib=${repeat_masking.repeat_source.rmlib} # provide an organism specific repeat library in fasta format for RepeatMasker
#else
rmlib= # provide an organism specific repeat library in fasta format for RepeatMasker
#end if

#if $repeat_masking.repeat_source.repeat_protein
repeat_protein=${repeat_masking.repeat_source.repeat_protein} # provide a fasta file of transposable element proteins for RepeatRunner
#else
repeat_protein= # provide a fasta file of transposable element proteins for RepeatRunner

                  </when>
                </conditional>
                <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
              </when>
              <when value="library">
                <param name="rmlib" type="data" format="fasta" label="Transposable element sequences for RepeatRunner" optional="True" />
                <param name="repeat_protein" type="data" format="fasta" label="Transposable element protein sequences for RepeatRunner" optional="True" />
                <param name="rm_gff" type="data" format="gff" label="Pre-identified repeat elements from an external GFF file" optional="True" />
                <param name="softmask" type="boolean" truevalue="1" falsevalue="0" checked="true" label="Use soft-masking rather than hard-masking in BLAST" help="i.e. seg and dust filtering"/>
              </when>
              <when value="no"/>
            </conditional>
        </section>