comparison cmsearch.xml @ 6:c650ee099c51 draft

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5:2b3adbe83979

    <parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile,multiple_alignment_output"></parallelism>
    <requirements>
        <requirement type="package" version="1.1rc4">infernal</requirement>
    </requirements>
    <command>
        ##TODO reformat the tabular-output: 
        ## -"Each line consists of 18 space-delimited fields followed by a free text target sequence description, as follows:"
        ## remove line that starts with #

        cmsearch 
            --cpu 12
            -o /dev/null
            --tformat $seqdb.ext ##target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip 

            $notrunc
            $max
            $nohmm
            $mid
            $bitscore_thresholds
            --tblout $outfile
            $g
            #if $A:
                $A $multiple_alignment_output
            #end if

            #if $inclusion_thresholds_opts.inclusion_thresholds_selector == "--incE":
                --incE $inclusion_thresholds_opts.incE
            #else:
                --incT $inclusion_thresholds_opts.incT
            #end if

            #if $reporting_thresholds_opts.reporting_thresholds_selector == "-E":
                -E $reporting_thresholds_opts.E
            #else:
                -T $reporting_thresholds_opts.T
            #end if

            #if $cm_opts.cm_opts_selector == "db":
                $cm_opts.database.fields.path
            #else:
                $cm_opts.cmfile
            #end if

            $seqdb


            2>&1
    </command>
        <inputs>

            <param name="seqdb" type="data" format="fasta" label="Sequence database"/>

            <conditional name="inclusion_thresholds_opts">
                <param name="inclusion_thresholds_selector" type="select" label="Inclusion thresholds"
                help="Inclusion thresholds are stricter than reporting thresholds. Inclusion thresholds control which hits are considered to be reliable enough to be included in an output alignment or in a possible subsequent search round, or marked as significant (”!”) as opposed to questionable (”?”) in hit output.">
                    <option value="--incE" selected="true">Use E-value</option>
                    <option value="--incT">Use bit score</option>
                </param>
                <when value="--incE">
                    <param name="incE" type="float" value="0.01" size="5" label="Use E-value" help="of &lt;= X as the hit inclusion threshold.">
                        <sanitizer>
                            <valid initial="string.printable">
                                <remove value="&apos;"/>

                            </valid>
                        </sanitizer>
                    </param>
                </when>
            </conditional>


            <!-- Options controlling reporting thresholds -->

            <conditional name="reporting_thresholds_opts">
                <param name="reporting_thresholds_selector" type="select" label="reporting thresholds"
                help="Reporting thresholds control which hits are reported in output files">
                    <option value="-E" selected="true">Use E-value</option>
                    <option value="-T">Use bit score</option>
                </param>
                <when value="-E">
                    <param name="E" type="float" value="10.0" size="5" label="Use E-value" help="of &lt;= X as the hit reporting threshold. The default is 10.0, meaning that on average, about 10 false positives will be reported per query, so you can see the top of the noise and decide for yourself if it’s really noise.">
                        <sanitizer>
                            <valid initial="string.printable">
                                <remove value="&apos;"/>

                </when>
            </conditional>

            <param name="A" truevalue="-A" falsevalue="" checked="False" type="boolean" 
                label="Save a multiple alignment of all significant hits" help="... those satisfying inclusion thresholds"/>


        </inputs>
    <outputs>

        <data format="tabular" name="outfile" label="cmsearch on ${on_string}"/>

6:c650ee099c51

    <parallelism method="multi" split_inputs="seqdb" split_mode="to_size" split_size="100" shared_inputs="" merge_outputs="outfile,multiple_alignment_output"></parallelism>
    <requirements>
        <requirement type="package" version="1.1rc4">infernal</requirement>
    </requirements>
    <command>
        temp_tabular_output=$(mktemp);

        cmsearch 
            --cpu 12
            -o /dev/null
            --tformat $seqdb.ext ##target format: fasta, embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip 

            $notrunc
            $max
            $nohmm
            $mid
            $bitscore_thresholds
            --tblout $temp_tabular_output
            $g
            #if $A:
                $A $multiple_alignment_output
            #end if

            #if $inclusion_thresholds_opts.inclusion_thresholds_selector == "--incE":
                --incE $inclusion_thresholds_opts.incE
            #elif $inclusion_thresholds_opts.inclusion_thresholds_selector == "--incT":
                --incT $inclusion_thresholds_opts.incT
            #end if

            #if $reporting_thresholds_opts.reporting_thresholds_selector == "-E":
                -E $reporting_thresholds_opts.E
            #elif $reporting_thresholds_opts.reporting_thresholds_selector == "-T":
                -T $reporting_thresholds_opts.T
            #end if

            #if $cm_opts.cm_opts_selector == "db":
                $cm_opts.database.fields.path
            #else:
                $cm_opts.cmfile
            #end if

            $seqdb
            2>&1
            ;

            sed -e 's/#.*$//' -e '/^$/d' -e 's/ /\t/g' -e 's/\t/ /18g' $temp_tabular_output > $outfile

    </command>
        <inputs>

            <param name="seqdb" type="data" format="fasta" label="Sequence database"/>

            <conditional name="inclusion_thresholds_opts">
                <param name="inclusion_thresholds_selector" type="select" label="Inclusion thresholds"
                help="Inclusion thresholds are stricter than reporting thresholds. Inclusion thresholds control which hits are considered to be reliable enough to be included in an output alignment or in a possible subsequent search round, or marked as significant (”!”) as opposed to questionable (”?”) in hit output.">
                    <option value="" selected="true">default</option>
                    <option value="--incE">Use E-value</option>
                    <option value="--incT">Use bit score</option>
                </param>
                <when />
                <when value="--incE">
                    <param name="incE" type="float" value="0.01" size="5" label="Use E-value" help="of &lt;= X as the hit inclusion threshold.">
                        <sanitizer>
                            <valid initial="string.printable">
                                <remove value="&apos;"/>

                            </valid>
                        </sanitizer>
                    </param>
                </when>
            </conditional>

            <!-- Options controlling reporting thresholds -->

            <conditional name="reporting_thresholds_opts">
                <param name="reporting_thresholds_selector" type="select" label="reporting thresholds"
                help="Reporting thresholds control which hits are reported in output files">
                    <option value="" selected="true">default</option>
                    <option value="-E">Use E-value</option>
                    <option value="-T">Use bit score</option>
                </param>
                <when />
                <when value="-E">
                    <param name="E" type="float" value="10.0" size="5" label="Use E-value" help="of &lt;= X as the hit reporting threshold. The default is 10.0, meaning that on average, about 10 false positives will be reported per query, so you can see the top of the noise and decide for yourself if it’s really noise.">
                        <sanitizer>
                            <valid initial="string.printable">
                                <remove value="&apos;"/>

                </when>
            </conditional>

            <param name="A" truevalue="-A" falsevalue="" checked="False" type="boolean" 
                label="Save a multiple alignment of all significant hits" help="... those satisfying inclusion thresholds"/>

        </inputs>
    <outputs>

        <data format="tabular" name="outfile" label="cmsearch on ${on_string}"/>