comparison samtools_view.xml @ 6:ff313de5f7f4 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"

5:90944a49ad05

        ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
        ## then sort the output by coordinate, 
        #if not $input.is_of_type('bam') and $outtype == 'bam':
            && samtools sort
                -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
                -O bam
                -o 'tmpsam'
                outfile
                && mv tmpsam outfile
            #if $adv_output.outputpassing == 'yes':
                && samtools sort
                    -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T sorttemp
                    -O bam
                    -o 'tmpsam'
                    inv_outfile
                && mv tmpsam inv_outfile
            #end if

                <param name="ref" format="fasta,fasta.gz" optional="true" type="data" label="Reference file"/>
            </when>
            <when value="cached">
                <param name="ref" type="select" label="Using reference genome">
                    <options from_data_table="fasta_indexes">
                        <filter column="1" key="dbkey" ref="input" type="data_meta" />
                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
                    </options>
                </param>
            </when>
        </conditional>

6:ff313de5f7f4

        ## if data is converted from an unsorted file (SAM, CRAM, or unsorted BAM) to BAM
        ## then sort the output by coordinate, 
        #if not $input.is_of_type('bam') and $outtype == 'bam':
            && samtools sort
                -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
                -O bam
                -o 'tmpsam'
                outfile
                && mv tmpsam outfile
            #if $adv_output.outputpassing == 'yes':
                && samtools sort
                    -@ \$addthreads -m \${GALAXY_MEMORY_MB:-768}M -T "\${TMPDIR:-.}"
                    -O bam
                    -o 'tmpsam'
                    inv_outfile
                && mv tmpsam inv_outfile
            #end if

                <param name="ref" format="fasta,fasta.gz" optional="true" type="data" label="Reference file"/>
            </when>
            <when value="cached">
                <param name="ref" type="select" label="Using reference genome">
                    <options from_data_table="fasta_indexes">
                        <filter column="dbkey" key="dbkey" ref="input" type="data_meta" />
                        <validator message="No reference genome is available for the build associated with the selected input dataset" type="no_options" />
                    </options>
                </param>
            </when>
        </conditional>