comparison seqkit_locate.xml @ 1:6510652376b1 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit e0bd99c950e2c5f403474fad5af0be3829c93607

0:642d73815dd1

    $advanced_options.use_fmi
#end if
$advanced_options.non_greedy
$advanced_options.only_positive_strand
$advanced_options.id_ncbi
'${input_identifier}'
> '$output'
]]></command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>

            </when>
            <when value="file">
                <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/>
            </when>
        </conditional>
        <param name="output_mode" type="select" label="Output mode">
            <option value="">Tabular (default format)</option>
            <option value="--gtf">GTF</option>
            <option value="--bed">BED6</option>
        </param>

            <section name="advanced_options">
                <param name="use_fmi" value="true"/>
            </section>
            <output name="output" file="locate_output3.gtf" ftype="gtf"/>
        </test>
    </tests>
    <help>
.. class:: infomark

**Purpose**

1:6510652376b1

    $advanced_options.use_fmi
#end if
$advanced_options.non_greedy
$advanced_options.only_positive_strand
$advanced_options.id_ncbi
--seq-type $seq_type
'${input_identifier}'
> '$output'
]]></command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz" label="Input file"/>

            </when>
            <when value="file">
                <param argument="--pattern-file" type="data" format="fasta" label="Pattern/motif file"/>
            </when>
        </conditional>
        <param argument="--seq-type" type="select" label="Sequence type" help="For automatic detection, it automatically detect by the first sequence. Default: auto">
            <option value="auto">Automatic detection</option>
            <option value="dna">DNA</option>
            <option value="rna">RNA</option>
            <option value="protein">Protein</option>
        </param>
        <param name="output_mode" type="select" label="Output mode">
            <option value="">Tabular (default format)</option>
            <option value="--gtf">GTF</option>
            <option value="--bed">BED6</option>
        </param>

            <section name="advanced_options">
                <param name="use_fmi" value="true"/>
            </section>
            <output name="output" file="locate_output3.gtf" ftype="gtf"/>
        </test>
        <test expect_num_outputs="1">
            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
            <conditional name="conditional_pattern">
                <param name="mode" value="expression"/>
                <param name="pattern" value="ATAGAT"/>
            </conditional>
            <param name="seq_type" value="dna"/>
            <section name="advanced_options">
                <param name="max_mismatch" value="1"/>
            </section>
            <output name="output" file="locate_output1.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
.. class:: infomark

**Purpose**