comparison getfastaBed.xml @ 42:841fb4dc3ab3 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 4046c1da68a09c7a3c275f6fe890ec71470fd74d"

41:7ab85ac5f64b

<tool id="bedtools_getfastabed" name="bedtools GetFastaBed" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>use intervals to extract sequences from a FASTA file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />

    ln -s '${fasta_file}.fai' 'input.fasta.fai' &&
#end if
ln -s '$fasta_file' 'input.fasta' &&
bedtools getfasta
$name
$tab
$strand
$split
-fi 'input.fasta'
-bed '$input'

                  <options from_data_table="fasta_indexes" />
               </param>
            </when>
        </conditional>
        <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
            label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
        <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
            label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
            label="Force strandedness"

        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="tab" value="False" />
            <param name="split" value="False" />
            <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
        </test>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="tab" value="True" />
            <param name="split" value="False" />
            <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

42:841fb4dc3ab3

<tool id="bedtools_getfastabed" name="bedtools getfasta" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>use intervals to extract sequences from a FASTA file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools" />

    ln -s '${fasta_file}.fai' 'input.fasta.fai' &&
#end if
ln -s '$fasta_file' 'input.fasta' &&
bedtools getfasta
$name
$nameOnly
$tab
$strand
$split
-fi 'input.fasta'
-bed '$input'

                  <options from_data_table="fasta_indexes" />
               </param>
            </when>
        </conditional>
        <param argument="-name" type="boolean" truevalue="-name" falsevalue="" checked="false"
            label="Use the 'name' column in the BED file and the coordinates for the FASTA headers in the output FASTA file" />
        <param argument="-nameOnly" type="boolean" truevalue="-nameOnly" falsevalue="" checked="false"
            label="Use the 'name' column in the BED file for the FASTA headers in the output FASTA file" />
        <param argument="-tab" type="boolean" truevalue="-tab" falsevalue="" checked="false"
            label="Report extract sequences in a tab-delimited format instead of in FASTA format" />
        <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
            label="Force strandedness"

        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="tab" value="False" />
            <param name="split" value="False" />
            <param name="nameOnly" value="False" />
            <output name="output" file="getfastaBed_result1.bed" ftype="fasta" />
        </test>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="tab" value="True" />
            <param name="split" value="False" />
            <param name="nameOnly" value="False" />
            <output name="output" file="getfastaBed_result2.tabular" ftype="tabular" />
        </test>
        <test>
            <param name="input" value="nucBed1.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="tab" value="False" />
            <param name="split" value="False" />
            <param name="name" value="True" />
            <output name="output" file="getfastaBed_result3.bed" ftype="fasta" />
        </test>
        <test>
            <param name="input" value="nucBed2.bed" ftype="bed" />
            <param name="fasta" value="nucBed1.fasta" ftype="fasta" />
            <param name="tab" value="False" />
            <param name="split" value="False" />
            <param name="nameOnly" value="True" />
            <output name="output" file="getfastaBed_result4.bed" ftype="fasta" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**