annotate macros.xml @ 2:dd991ca3d8ce draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/locarna commit 80c721dcfe02a2b8baf8e2c64b76cbcd71b23d86

<macros>
    <token name="@VERSION@">1.9.0</token>

    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@VERSION@">locarna</requirement>
        </requirements>
    </xml>

    <xml name="stdio">
        <stdio>
            <exit_code range="1:" />
        </stdio>
    </xml>

    <xml name="version">
        <version_command>
            <![CDATA[
                     mlocarna --version
            ]]>
        </version_command>
    </xml>

    <xml name="bed_anchors">
        <conditional name="bed_anchors">
            <param name="bed_anchors_selector" type="select" label="Anchor constraints"
                   help="Anchor constraints in bed format specify positions of
                         named anchor regions per sequence. The sequence names
                         ('contig' names have to correspond to the fasta input
                         sequence names. Anchor names must be unique per sequence
                         and regions of the same name for different sequences
                         must have the same length. This constrains the alignment
                         to align all regions of the same name.">
                <option value="no">Don't load anchor constraints from
                bed file</option>
                <option value="yes">Load anchor constraints from bed
                file</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param name="bed_anchors_file" type="data" format="tabular" 
                       label="Anchor constraint specification in bed format"
                       />
            </when>
        </conditional>
    </xml>
    
    <xml name="common_scoring_parameters">
        <param name="struct_weight" argument="struct-weight"
               label="Structure weight" type="integer" 
               value="200" min="0" max="800" />
        <param name="indel_opening" argument="indel-opening"
               label="Indel opening score" type="integer"
               value="-500" max="0" min="-1500" />
        <param argument="indel" label="Indel score" type="integer" 
               value="-350" min="-1000" max="0" />
        <param argument="tau" type="integer" value="50"
               min="0" max="200"
               label="Sequence contribution at structure match in percent"/> 

        <conditional name="sequence_score">
            <param name="sequence_score_selector" type="select" label="Type of sequence score contribution">
                <option value="ribofit">Use ribofit</option>
                <option value="ribosum">Use RIBOSUM85_60</option>
                <option value="match">Simple match/mismatch costs</option>
            </param>
            <when value="ribofit" />
            <when value="ribosum" />
            <when value="match">
                <param name="match" type="integer" value="50" 
                       min="0" max="400"
                       label="Match score" />
                <param name="mismatch" type="integer" value="0" 
                       min="-400" max="0"
                       label="Mismatch score" />
            </when>
        </conditional>
    </xml>

    <xml name="plfolding_parameters">
        <param name="plfold_span" argument="--plfold-span" 
               type="integer" value="150" min="-1" max="400" 
               label="Maximum basepair span by RNAplfold (local folding); -1 for global folding" />
        
        <param name="plfold_winsize" argument="--plfold-winsize"
               type="integer" value="300"  min="-1" max="800" 
               label="Window size for local folding" />
    </xml>
    
    <xml name="common_folding_parameters">
        <param name="rnafold_temperature" argument="rnafold-temperature"
               type="float" value="37.0" min="10" max="50"
               label="Temperature for RNAfold (RNAfold's -T option)" />
    </xml>

    <token name="@SCORING_ARGS@">
        ## -------------------- scoring parameters
        --indel $Scoring.indel
        --indel-opening $Scoring.indel_opening
        --struct-weight $Scoring.struct_weight
        --tau $Scoring.tau
        
        #if str($Scoring.sequence_score.sequence_score_selector) == "match"
            --match $Scoring.sequence_score.match
            --mismatch $Scoring.sequence_score.mismatch
        #elif str($Scoring.sequence_score.sequence_score_selector) == "ribosum"
            --use-ribosum true
        #elif str($Scoring.sequence_score.sequence_score_selector) == "ribofit"
            --ribofit true
        #end if
    </token>

    <token name="@FOLDING_ARGS@">
        ## -------------------- folding parameters
        #if float($Folding.rnafold_temperature) != 37.0
            --rnafold-temperature $Folding.rnafold_temperature
        #end if
    </token>

    <token name="@HEURISTIC_ARGS@">
        ## -------------------- heuristic parameters
        -p $Heuristics.min_prob

        #if str($Heuristics.max_diff_mode.max_diff_mode_selector) == "off"
            --max-diff -1
        #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff"
            --max-diff $Heuristics.max_diff_mode.max_diff
        #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-at-am"
            --max-diff -1
            --max-diff-at-am $Heuristics.max_diff_mode.max_diff_at_am
        #elif str($Heuristics.max_diff_mode.max_diff_mode_selector) == "max-diff-aln"
            --max-diff $Heuristics.max_diff_mode.max_diff
            --max-diff-aln '$Heuristics.max_diff_mode.max_diff_aln'
            $Heuristics.max_diff_mode.max_diff_relax
        #end if
        
        --max-diff-am $Heuristics.max_diff_am
    
        #if float($Heuristics.max_bps_length_ratio) > 0.0
            --max-bps-length-ratio $Heuristics.max_bps_length_ratio
        #end if
    </token>

    <token name="@HEURISTIC_SPARSE_ARGS@">
           --prob-unpaired-in-loop $alignment_mode.HeuristicsSparse.prob_unpaired_in_loop_threshold
           --prob-basepair-in-loop $alignment_mode.HeuristicsSparse.prob_basepair_in_loop_threshold

    </token>

    <token name="@CONSTRAINT_ARGS@">
        ## -------------------- constraint parameters
        $Constraints.lonely_pairs

        #if $Constraints.maxBPspan != -1
            --maxBPspan $Constraints.maxBPspan
        #end if

        $Constraints.ignore_constraints
    </token>

    <token name="@STDOUT_ARGS@">
        $stdout_verbosity
        
        #if str($stdout_verbosity) != "--quiet":
            > '$stdout'
        #end if
    </token>

    <xml name="max_diff_parameters_selector">
        <param name="max_diff_mode_selector" type="select"
               label="Restrict alignable positions by maximum difference" 
               help="(max-diff*)">
            <option value="off">Off</option>
            <option value="max-diff" selected="True">Maximal difference of aligned positions</option>
            <option value="max-diff-at-am">Maximal difference of aligned positions at arc matches</option> 
            <yield />
        </param>
    </xml>
    
    <xml name="max_diff_parameters_standard_cases">
        <when value="off" />
        <when value="max-diff">
            <param  name="max_diff" argument="max-diff" type="integer"
                    value="60" min="-1" max="300"
                    label="Maximal difference of aligned positions" />
        </when>
        <when value="max-diff-at-am">
            <param  name="max_diff_at_am" argument="max-diff-at-am" type="integer" 
                    value="60" min="-1" max="300"
                    label="Maximal difference of aligned positions,
                           only at arc match positions" />
        </when>
    </xml>

    <xml name="max_diff_parameters">
        <conditional name="max_diff_mode">
            <expand macro="max_diff_parameters_selector" />
            <expand macro="max_diff_parameters_standard_cases" />
        </conditional>
    </xml>

    <xml name="max_diff_parameters_aln">
        <conditional name="max_diff_mode">
            <expand macro="max_diff_parameters_selector">
                <option value="max-diff-aln">Maximal difference to a reference alignment</option>
            </expand>
            <expand macro="max_diff_parameters_standard_cases" />
            <when value="max-diff-aln">
                <param name="max_diff_aln" argument="max-diff-aln" type="data" format="clustal"
                       label="Reference alignment"
                       />
                <param  name="max_diff" argument="max-diff" type="integer"
                        value="60" min="-1" max="300"
                        label="Maximal difference of aligned positions" />
                <param name="max_diff_relax" argument="max-diff-relax" type="boolean"
                       truevalue="--max-diff-relax" falsevalue=""
                       checked="False"
                       label="Relax deviation constraints in multiple
                              aligmnent."
                       />
            </when>
        </conditional>
    </xml>

    <xml name="common_heuristic_parameters">
        <param  name="min_prob" argument="min-prob" type="float" value="0.0005" 
                min="0.0" max="0.2"
                label="Minimal / cutoff probability" /> 
    
        <param  name="max_diff_am" argument="max-diff-am" 
                type="integer" value="30" 
                min="-1" max="300"
                label="Maximal difference for sizes of matched arcs (-1=off)" />
        
        <param  name="max_bps_length_ratio" argument="max-bps-length-ratio"
                type="float" value="0.0" min="0.0" max="10.0" 
                label="Maximal ratio 'number of considered base pairs' by
                       'sequence length' (default: 0.0 = no effect)" />
    </xml>
    
    <xml name="common_heuristic_parameters_sparse">
        <param  name="prob_unpaired_in_loop_threshold" argument="prob-unpaired-in-loop-threshold" type="float" value="0.00005" 
                min="0.0" max="0.2"
                label="Probability threshold for unpaired bases in loops" /> 

        <param  name="prob_basepair_in_loop_threshold" argument="prob-basepair-in-loop-threshold" type="float" value="0.0001" 
                min="0.0" max="0.2"
                label="Probability threshold for base pairs in loops" />       
    </xml>
    
    <xml name="in_loop_ratio_parameters">
        <param  name="max_uil_length_ratio" argument="max-uil-length-ratio"
                type="float" value="0.0" min="0.0" max="10.0" 
                label="Maximal ratio 'number considered unpaired bases in loops' by
                       'sequence length' (default: 0.0; no effect)" />
        
        <param  name="max_bpil_length_ratio" argument="max-bpil-length-ratio"
                type="float" value="0.0" min="0.0" max="10.0" 
                label="Maximal ratio 'number of considered base pairs in loops'
                       by 'sequence length' (default: 0.0; no effect)" />
    </xml>

    <xml name="exparnap_in_loop_parameters">
        <param  name="prob_unpaired_in_loop_threshold"
                argument="prob_unpaired_in_loop_threshold"
                type="float" value="0.01" min="0.0" max="1.0" 
                label="Probability threshold for unpaired bases in loops" />
        <param  name="prob_basepair_in_loop_threshold"
                argument="prob_basepair_in_loop_threshold"
                type="float" value="0.01" min="0.0" max="1.0" 
                label="Probability threshold for base pairs in loops" />
    </xml>

    <xml name="alifold_consensus_parameter">
        <param  name="alifold_consensus_dp" argument="alifold-consensus-dp" 
                type="boolean" checked="False" 
                truevalue="--alifold-consensus-dp" falsevalue=""
                label="Compute consensus dot plot by alifold" />
    </xml>
    
    <xml name="common_constraint_parameters">
        <param name="lonely_pairs" type="boolean" truevalue="--LP" falsevalue="--noLP" 
               checked="false" label="Allow lonely base-pairs" help="(--LP/--noLP)" />
        <param name="maxBPspan" argument="--maxBPspan" 
               type="integer" value="-1" min="-1" max="400" 
               label="Maximum basepair span by RNAfold; -1 for arbitrary span" />
        <param name="ignore_constraints" argument="ignore-constraints"
               type="boolean" checked="false" truevalue="--ignore-constraints" falsevalue=""
               help="Ignore all anchor and structure constraints given
                     in the fasta(-ish) input." />
    </xml>

    <xml name="standard_outupt">
        <data format="txt" name="stdout" label="${tool.name} std out on ${on_string}">
            <filter>stdout_verbosity != '--quiet'</filter>
        </data>
    </xml>

    <xml name="mlocarna_outputs">
        <expand macro="standard_outupt" />
        <data format="clustal" name="clustal" from_work_dir="mlocarna_results/results/result.aln"
              label="${tool.name} alignment (annotated clustal) on ${on_string}">
            <filter>'clustal' in outputs</filter>
        </data>
        <data format="clustal" name="clustal_strict" 
              from_work_dir="mlocarna_results/results/result.strict-aln"
              label="${tool.name} alignment (clustal) on ${on_string}">
            <filter>'clustal_strict' in outputs</filter>
        </data>
        <data format="stockholm" name="stockholm" from_work_dir="mlocarna_results/results/result.stk"
              label="${tool.name} alignment (stockholm) on ${on_string}">
            <filter>'stockholm' in outputs</filter>
        </data>
        <data format="txt" name="pp"
              from_work_dir="mlocarna_results/results/result.pp"
              label="${tool.name} alignment (PP 2.0) on ${on_string}">
            <filter>'pp' in outputs</filter>
        </data>
        <data format="tar.gz" name="mlocarna_results_tgz"
              label="${tool.name} results archive on ${on_string}">
            <filter>'mlocarna_results' in outputs</filter>
        </data>
    </xml>

    <xml name="citations">
        <citations>
            <citation type="doi">10.1371/journal.pcbi.0030065</citation>
            <citation type="doi">10.1261/rna.029041.111</citation>
            <citation type="doi">10.1093/bioinformatics/btv185</citation>
            <citation type="doi">10.1186/s12859-014-0404-0</citation>
        </citations>
    </xml>



</macros>