annotate segalign_output_options.xml @ 8:150de8a3954a draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 11132ef8b4103731b6f5860ea736bf332a06e303

<macros>
    <xml name="segalign_output_options">
        <conditional name="format">
            <param name="format_selector" type="select" display="radio" label="Specify the output format">
                <option value="bam">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" selected="true">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">BAM</option>
                    <option value="softsam">soft-clipped BAM</option>
                    <option value="sam-">BAM without header</option>
                    <option value="softsam-">soft-clipped BAM without header</option>
                </param>
            </when>
            <when value="general_def">
                <!-- Do nothing -->
            </when>
            <when value="general_full">
                <param name="fields" type="select" display="checkboxes" multiple="true" label="Select which fields to include" argument="--format=general-[:fields]">
                    <option value="score" selected="true">score: Score of the alignment block</option>
                    <option value="name1" selected="true">name1: Name of the target sequence</option>
                    <option value="number1">number1: Number of the target sequence within the target file</option>
                    <option value="strand1" selected="true">strand1: Target sequence strand </option>
                    <option value="size1" selected="true">size1: Size of the entire target sequence</option>
                    <option value="start1">start1: Starting position of the alignment block in the target, origin-one</option>
                    <option value="zstart1" selected="true">zstart1: Starting position of the alignment block in the target, origin-zero</option>
                    <option value="end1" selected="true">end1: Ending position of the alignment block in the target</option>
                    <option value="length1">length1: Length of the alignment block in the target (excluding gaps)</option>
                    <option value="text1">text1: Aligned characters in the target, including gap characters</option>
                    <option value="qalign1">qalign1: The target quality sequence (if there is one) correpsonding to aligned characters</option>
                    <option value="nucs1">nucs1: The entire target sequence</option>
                    <option value="name2" selected="true">name2: Name of the query sequence</option>
                    <option value="number2">number2: Number of the query sequence within the query file</option>
                    <option value="strand2" selected="true">strand2: Query sequence strand</option>
                    <option value="size2" selected="true">size2: Size of the entire query sequence</option>
                    <option value="start2">start2: Starting position of the alignment block in the query, origin-one</option>
                    <option value="zstart2" selected="true">zstart2: Starting position of the alignment block in the query, origin-one</option>
                    <option value="end2" selected="true">end2: Ending position of the alignment block in the query</option>
                    <option value="length2">length2: Length of the alignment block in the query (excluding gaps)</option>
                    <option value="text2">text2: Aligned characters in the query, including gap characters</option>
                    <option value="qalign2">qalign2: The query quality sequence (if there is one) correpsonding to aligned characters</option>
                    <option value="nucs2">nucs2: The entire query sequence</option>
                    <option value="nmatch">nmatch: Match count</option>
                    <option value="nmismatch">nmismatch: Mismatch count</option>
                    <option value="ncolumn">ncolumn: Number of columns in the block. This includes matches, mismatches (substitutions), and gaps</option>
                    <option value="npair">npair: Number of aligned bases in the block that are matches or mismatches (substitutions)</option>
                    <option value="ngap">ngap: Gap count, the number of gaps in the block, counting each run of gapped columns as a single gap</option>
                    <option value="cgap">cgap: Gap column count, the number of gaps in the block, counting each gapped column as a separate gap</option>
                    <option value="diff">diff: Differences between what would be written for text1 and text2</option>
                    <option value="cigar">cigar: A CIGAR-like representation of the alignment’s path</option>
                    <option value="cigarx">cigarx: Same as cigar, but uses a newer syntax that distinguishes matches from substitutions</option>
                    <option value="identity" selected="true">identity: Fraction of aligned bases in the block that are matches </option>
                    <option value="idfrac">idfrac: Fraction of aligned bases in the block that are matches </option>
                    <option value="id%" selected="true">id% Fraction of aligned bases in the block that are matches (as %)</option>
                    <option value="blastid%">blastid%: Fraction of the alignment block that is matches, as would be reported by NCBI BLAST</option>
                    <option value="continuity">continuity: Rate of non-gaps (non-indels) in the alignment block</option>
                    <option value="confrac">confrac: Rate of non-gaps (non-indels) in the alignment block (as fraction)</option>
                    <option value="con%">con%: Rate of non-gaps (non-indels) in the alignment block (as %)</option>
                    <option value="coverage" selected="true">coverage: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block</option>
                    <option value="covfrac">covfrac: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as fraction)</option>
                    <option value="cov%" selected="true">cov%: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as %)</option>
                    <option value="diagonal">diagonal: The diagonal of the start of the alignment block in the DP matrix, expressed as an identifying number start1-start2</option>
                    <option value="shingle">shingle: A measurement of the shingle overlap between the target and the query</option>
                    <option value="number">number: The alignment number, counted as alignments are written to output (1-base)</option>
                    <option value="znumber">znumber: The alignment number, counted as alignments are written to output (0-base)</option>
                    <sanitizer invalid_char="">
                        <valid initial="string.letters,string.digits">
                            <add value="%"/>
                        </valid>
                    </sanitizer>
                </param>
            </when>
            <when value="maf">
                <param name="maf_type" type="select" display="radio" argument="--format=maf" label="Select MAF flavor" help="MAF is a multiple alignment format developed at UCSC">
                    <option value="maf">MAF</option>
                    <option value="maf+">MAF with additional stats</option>
                    <option value="maf-" selected="true">MAF without header and comments</option>
                </param>
            </when>
            <when value="blastn">
                <!-- Do nothing -->
            </when>
            <when value="differences">
                <!-- Do nothing -->
            </when>
        </conditional>
    </xml>
</macros>