comparison getfastaBed.xml @ 10:c78cf6fe3018 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 44bebb8a97d64015cbba59f0663e2541035112b6

9:2ab422b551df

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools getfasta
        $name
        $tab
        $strand
        $split
        -fi $fasta 
        -bed $input
        -fo $output
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
        <param format="fasta" name="fasta" type="data" label="Fasta file" />
        <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
            label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
            help="(-name)" />
        <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
            label="Report extract sequences in a tab-delimited format instead of in FASTA format"

10:c78cf6fe3018

    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        #if str( $fasta_source.fasta_source_selector ) == 'history':
          #set $fasta_file = $fasta_source.fasta
        #else
          #set $fasta_file = $fasta_source.fasta_id.fields.path
        #end if
        bedtools getfasta
        $name
        $tab
        $strand
        $split
        -fi '$fasta_file'
        -bed '$input'
        -fo '$output'
]]>
    </command>
    <inputs>
        <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
        
        <conditional name="fasta_source">
            <param name="fasta_source_selector" type="select" label="Choose the source for the fasta file">
                <option value="history" selected="True">History</option>
                <option value="preloaded">Server indexed files</option>
            </param>
            <when value="history">
                <param name="fasta" format="fasta" type="data" label="Fasta file" />
            </when>
            <when value="preloaded">
               <param name="fasta_id" type="select">
                  <options from_data_table="all_fasta" />
               </param> 
            </when>
        </conditional>
        <param name="name" type="boolean" checked="false" truevalue="-name" falsevalue=""
            label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file"
            help="(-name)" />
        <param name="tab" type="boolean" checked="false" truevalue="-tab" falsevalue=""
            label="Report extract sequences in a tab-delimited format instead of in FASTA format"