comparison align_and_estimate_abundance.xml @ 15:56162e446004 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit f5736e63d4d4210c33eea4a1985508466c3c168d"

14:983552d5822d

        --transcripts input.fa

        --est_method $method.est_method
        #if $method.est_method == "RSEM":
            --aln_method $method.aln_method
        #else if $method.est_method == "salmon":
            --salmon_idx_type $method.salmon_idx_type
        #end if

        #if $inputs.paired_or_single == "paired":

            #if $inputs.left_input.is_of_type('fasta'):

                    <option value="bowtie">Bowtie</option>
                    <option value="bowtie2">Bowtie2</option>
                </param>
            </when>
            <when value="salmon">
                <param type="select" name="salmon_idx_type" argument="--salmon_idx_type" label="Index type">
                    <option value="quasi">Quasi</option>
                    <option value="fmd">FMD</option>
                </param>
            </when>
            <when value="kallisto">
            </when>
        </conditional>

15:56162e446004

        --transcripts input.fa

        --est_method $method.est_method
        #if $method.est_method == "RSEM":
            --aln_method $method.aln_method
        #end if

        #if $inputs.paired_or_single == "paired":

            #if $inputs.left_input.is_of_type('fasta'):

                    <option value="bowtie">Bowtie</option>
                    <option value="bowtie2">Bowtie2</option>
                </param>
            </when>
            <when value="salmon">
            </when>
            <when value="kallisto">
            </when>
        </conditional>