comparison sRbowtie.xml @ 1:71b072cf5dde draft

planemo upload for repository https://bitbucket.org/drosofff/gedtools/

0:e8bdae1a2bdc

<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.0">
    <description>for FASTA small reads</description>
    <requirements>
        <requirement type="package" version="0.12.7">bowtie</requirement>
        <requirement type="package" version="0.1.18">samtools</requirement>
    </requirements>
    <command interpreter="python"> sRbowtie.py --input $input
                                             --input-format $input.extension
                                             --method $method
                                             --v-mismatches $v_mismatches

            <when value="history">
                <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
            </when>
        </conditional>
        <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select">
            <option select="true" value="tabular">tabular</option>
            <option value="sam">sam</option>
            <option value="bam">bam</option>
        </param>
        <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
            <option select="true" value="No">No</option>
            <option value="al">aligned</option>
            <option value="unal">unaligned</option>
            <option value="al_and_unal">both aligned and unaligned</option>
        </param>
    </inputs>

            <param ftype="fasta" name="ownFile" value="297_reference.fa" />
            <param name="method" value="unique" />
            <param ftype="fasta" name="input" value="input.fa" />
            <param name="v_mismatches" value="1" />
            <param name="output_format" value="bam" />
            <output file="output.bam" ftype="bam" lines_diff="4" name="output" />
        </test>
        <test>
            <param name="genomeSource" value="history" />
            <param ftype="fasta" name="ownFile" value="297_reference.fa" />
            <param name="method" value="unique" />
            <param ftype="fastq" name="input" value="input.fastq" />
            <param name="v_mismatches" value="1" />
            <param name="output_format" value="bam" />
            <output file="output2.bam" ftype="bam" lines_diff="4" name="output" />
        </test>
    </tests>
    <help>

**What it does**

1:71b072cf5dde

<tool id="bowtieForSmallRNA" name="sRbowtie" version="1.1.1">
    <description>for FASTA small reads</description>
    <requirements>
        <requirement type="package" version="0.12.7">bowtie</requirement>
        <requirement type="package" version="1.2">samtools</requirement>
    </requirements>
    <command interpreter="python"> sRbowtie.py --input $input
                                             --input-format $input.extension
                                             --method $method
                                             --v-mismatches $v_mismatches

            <when value="history">
                <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" />
            </when>
        </conditional>
        <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select">
            <option selected="true" value="tabular">tabular</option>
            <option value="sam">sam</option>
            <option value="bam">bam</option>
        </param>
        <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select">
            <option selected="true" value="No">No</option>
            <option value="al">aligned</option>
            <option value="unal">unaligned</option>
            <option value="al_and_unal">both aligned and unaligned</option>
        </param>
    </inputs>

            <param ftype="fasta" name="ownFile" value="297_reference.fa" />
            <param name="method" value="unique" />
            <param ftype="fasta" name="input" value="input.fa" />
            <param name="v_mismatches" value="1" />
            <param name="output_format" value="bam" />
            <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
        </test>
        <test>
            <param name="genomeSource" value="history" />
            <param ftype="fasta" name="ownFile" value="297_reference.fa" />
            <param name="method" value="unique" />
            <param ftype="fastq" name="input" value="input.fastq" />
            <param name="v_mismatches" value="1" />
            <param name="output_format" value="bam" />
            <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" />
        </test>
    </tests>
    <help>

**What it does**