comparison galaxy/tools/config_builder/config_builder.xml @ 7:4bfb3a8dd955 draft

Bug fixes

6:a39471bf7d13

                        variant site"/>
                        <param name="minfrac" type="float" value="0.9" min="0" label="Minimum proportion of
                        variant evidence"/>
                    </when>
                </conditional>
                <param name="snp_fine" type="boolean" label="Consider SNP as a fine datatype"/>
                <param name="snp_threshold" type="integer" value="2500" min="0"
                       label="Correlation clustering threshold for MLST"/>
            </when>
        </conditional>

                        mutations when looking for novel alleles"/>
                        <param name="kt" type="integer" value="10" min="1" label="Minimum number of times a
                        kmer is seen to be considered present in the sample"/>
                    </when>
                </conditional>
                <param name="mlst_fine" type="boolean" label="Consider MLST as a fine datatype"/>
                <param name="mlst_threshold" type="integer" value="300" min="0"
                       label="Correlation clustering threshold for MLST"/>
            </when>
        </conditional>

        <conditional name="prince">
            <param name="prince_checkbox" type="boolean" label="Run PRINCE"/>
            <when value="true">
                <param name="cnv_fine" type="boolean" label="Consider CNV as a fine datatype"/>
                <param name="cnv_threshold" type="integer" value="100" min="0"
                       label="Correlation clustering threshold for CNV"/>
            </when>
        </conditional>

                        <param name="ksize" type="integer" value="31" min="1" label="kmer size"/>
                        <param name="unique_kmers" type="integer" value="0" min="0" label="Approximate number
                        of unique kmers in the input set"/>
                    </when>
                </conditional>
                <param name="kwip_fine" type="boolean" label="Consider kWIP as a fine datatype"/>
                <param name="kwip_threshold" type="float" value="0.4" min="0"
                       label="Correlation clustering threshold for kWIP"/>
            </when>
        </conditional>

        <conditional name="spotyping">
            <param name="spotyping_checkbox" type="boolean" label="Run SpoTyping"/>
            <when value="true">
                <param name="spoligo_fine" type="boolean" label="Consider spoligotype as a fine datatype"/>
                <param name="spoligo_threshold" type="integer" value="8" min="0"
                       label="Correlation clustering threshold for Spoligotyping"/>
            </when>
        </conditional>

7:4bfb3a8dd955

                        variant site"/>
                        <param name="minfrac" type="float" value="0.9" min="0" label="Minimum proportion of
                        variant evidence"/>
                    </when>
                </conditional>
                <param name="snp_fine" type="boolean" checked="true" falsevalue="" truevalue="--fine_snp"
                       label="Consider SNP as a fine datatype"/>
                <param name="snp_threshold" type="integer" value="2500" min="0"
                       label="Correlation clustering threshold for MLST"/>
            </when>
        </conditional>

                        mutations when looking for novel alleles"/>
                        <param name="kt" type="integer" value="10" min="1" label="Minimum number of times a
                        kmer is seen to be considered present in the sample"/>
                    </when>
                </conditional>
                <param name="mlst_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_mlst"
                       label="Consider MLST as a fine datatype"/>
                <param name="mlst_threshold" type="integer" value="300" min="0"
                       label="Correlation clustering threshold for MLST"/>
            </when>
        </conditional>

        <conditional name="prince">
            <param name="prince_checkbox" type="boolean" label="Run PRINCE"/>
            <when value="true">
                <param name="cnv_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_cnv"
                       label="Consider CNV as a fine datatype"/>
                <param name="cnv_threshold" type="integer" value="100" min="0"
                       label="Correlation clustering threshold for CNV"/>
            </when>
        </conditional>

                        <param name="ksize" type="integer" value="31" min="1" label="kmer size"/>
                        <param name="unique_kmers" type="integer" value="0" min="0" label="Approximate number
                        of unique kmers in the input set"/>
                    </when>
                </conditional>
                <param name="kwip_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_kwip"
                       label="Consider kWIP as a fine datatype"/>
                <param name="kwip_threshold" type="float" value="0.4" min="0"
                       label="Correlation clustering threshold for kWIP"/>
            </when>
        </conditional>

        <conditional name="spotyping">
            <param name="spotyping_checkbox" type="boolean" label="Run SpoTyping"/>
            <when value="true">
                <param name="spoligo_fine" type="boolean" checked="false" falsevalue="" truevalue="--fine_spoligo"
                       label="Consider spoligotype as a fine datatype"/>
                <param name="spoligo_threshold" type="integer" value="8" min="0"
                       label="Correlation clustering threshold for Spoligotyping"/>
            </when>
        </conditional>