comparison lastz.xml @ 5:ec4affe27298 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c"

4:0acd9701676b

<tool id="lastz_wrapper_2" name="LASTZ" version="1.3.2">
    <description>: align long sequences</description>
    <macros>
        <import>lastz_macros.xml</import>
    </macros>
    <requirements>

            '--format=${output_format.out.maf_type}'
        #elif str( $output_format.out.format ) == "blastn":
            --format=BLASTN-
        #elif str( $output_format.out.format ) == "general_full":
            '--format=general-:${output_format.out.fields}'
        #end if
        --action:target=multiple
        $output_format.rplot
        #if str( $output_format.out.format ) == "bam":
            | samtools sort -@\${GALAXY_SLOTS:-2} -O bam -o '${output}'
        #else:
            > '${output}'
        #end if
        #if $output_format.rplot:
            &&

                    <option value="bam" selected="true">BAM --format=sam)</option>
                    <option value="general_def">General default (--format=general)</option>
                    <option value="general_full">Customized general (‑‑format=general[:fields])</option>
                    <option value="maf">MAF (--format=maf)</option>
                    <option value="blastn">blastn (--format=BLASTN)</option>
                </param>
                <when value="bam">
                    <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package">
                        <option value="sam" selected="true">BAM</option>
                        <option value="softsam">soft-clipped BAM</option>

                    </param>
                </when>
                <when value="blastn">
                    <!-- Do nothing -->
                </when>
            </conditional>
            <param name="rplot" type="boolean" truevalue="--rdotplot=plot.r" falsevalue="" checked="false" argument="--rdotplot" label="Create a dotplot representation of alignments?" help="The dotplot is only useful if query and target contain exactly one sequence each"/>
        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads">
            <change_format>
                 <when input="output_format.out.format" value="bam" format="bam" />
                  <when input="output_format.out.format" value="maf" format="maf" />
            </change_format>
        </data>
        <data format="png" name="out_plot" label="${tool.name} on ${on_string}: dot plot">
            <filter>output_format['rplot']</filter>
        </data>

            <param name="query" ftype="fastq" value="chrM_mouse.fq" />
            <param name="strand" value="--strand=both" />
            <param name="format" value="blastn" />
            <output name="output" value="test5.out" />
        </test>
    </tests>

    <help><![CDATA[

**What is does**

5:ec4affe27298

<tool id="lastz_wrapper_2" name="LASTZ" version="1.3.3">
    <description>: align long sequences</description>
    <macros>
        <import>lastz_macros.xml</import>
    </macros>
    <requirements>

            '--format=${output_format.out.maf_type}'
        #elif str( $output_format.out.format ) == "blastn":
            --format=BLASTN-
        #elif str( $output_format.out.format ) == "general_full":
            '--format=general-:${output_format.out.fields}'
        #elif str( $output_format.out.format ) == "differences":
            '--format=differences'
        #end if
        --action:target=multiple
        $output_format.rplot
        #if str( $output_format.out.format ) == "bam":
            | samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}'
        #else:
            > '${output}'
        #end if
        #if $output_format.rplot:
            &&

                    <option value="bam" selected="true">BAM --format=sam)</option>
                    <option value="general_def">General default (--format=general)</option>
                    <option value="general_full">Customized general (‑‑format=general[:fields])</option>
                    <option value="maf">MAF (--format=maf)</option>
                    <option value="blastn">blastn (--format=BLASTN)</option>
                    <option value="differences">Differences (--format=differences)</option>
                </param>
                <when value="bam">
                    <param name="bam_options" type="select" display="radio" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package">
                        <option value="sam" selected="true">BAM</option>
                        <option value="softsam">soft-clipped BAM</option>

                    </param>
                </when>
                <when value="blastn">
                    <!-- Do nothing -->
                </when>
                <when value="differences">
                    <!-- Do nothing -->
                </when>
            </conditional>
            <param name="rplot" type="boolean" truevalue="--rdotplot=plot.r" falsevalue="" checked="false" argument="--rdotplot" label="Create a dotplot representation of alignments?" help="The dotplot is only useful if query and target contain exactly one sequence each"/>
        </section>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads">
            <change_format>
                <when input="output_format.out.format" value="bam" format="bam" />
                <when input="output_format.out.format" value="maf" format="maf" />
                <when input="output_format.out.format" value="differences" format="interval" />
            </change_format>
        </data>
        <data format="png" name="out_plot" label="${tool.name} on ${on_string}: dot plot">
            <filter>output_format['rplot']</filter>
        </data>

            <param name="query" ftype="fastq" value="chrM_mouse.fq" />
            <param name="strand" value="--strand=both" />
            <param name="format" value="blastn" />
            <output name="output" value="test5.out" />
        </test>
        <test>
            <param name="ref_source" value="cached" />
            <param name="target_2bit" value="phiX174" />
            <param name="query" value="phiX_split.fasta" />
            <param name="strand" value="--strand=both" />
            <param name="format" value="differences" />
            <output name="output" value="test6.out" />
        </test>
    </tests>

    <help><![CDATA[

**What is does**