Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy2 |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy1 (this tool) |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/1.1.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.5+galaxy1 |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.5.0 |
toolshed.g2.bx.psu.edu/repos/iuc/umi_tools_dedup/umi_tools_dedup/0.5.3.0 |
umi_tools_dedup |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
umi_tools | 1.1.2 | package |
samtools | 1.12 | package |
Additional information about this tool |
#if $input.is_of_type("sam"): ## TODO dedup has problems with SAM input in some cases ## https://github.com/CGATOxford/UMI-tools/issues/483 ## so convert it to sorted BAM for now ## #set $input_file = $input samtools sort --no-PG '$input' > 'input.bam' && samtools index -b 'input.bam' && #set $input_file = 'input.bam' #else: ln -sf '${input}' 'input.bam' && ln -sf '$input.metadata.bam_index' 'input.bam.bai' && #set $input_file = 'input.bam' #end if echo $input.ext && umi_tools dedup #if $output_stats_bool --output-stats=stats_outputs #end if $gd.buffer_whole_contig $gd.whole_contig $gd.multimapping_detection_method --extract-umi-method $bc.extract_umi_method #if str($bc.extract_umi_method) == 'read_id': --umi-separator '$bc.umi_separator' #else if str($bc.extract_umi_method) == 'tag': --umi-tag '$bc.umi_tag' #if $bc.umi_tag_split != '' --umi-tag-split '$bc.umi_tag_split' #end if #if $bc.umi_tag_delimiter != '' --umi-tag-delimiter '$bc.umi_tag_delimiter' #end if --cell-tag '$bc.cell_tag' #if $bc.cell_tag_split != '' --cell-tag-split '$bc.cell_tag_split' #end if #if $bc.cell_tag_delimiter != '' --cell-tag-delimiter '$bc.cell_tag_delimiter' #end if #end if --method $umi.method --edit-distance-threshold $umi.edit_distance_threshold $umi.spliced_is_unique --soft-clip-threshold $umi.soft_clip_threshold $umi.read_length --mapping-quality $sambam.mapping_quality --unmapped-reads $sambam.unmapped_reads #if $sambam.chimeric_pairs --chimeric-pairs $sambam.chimeric_pairs #end if #if $sambam.unpaired_reads --unpaired-reads $sambam.unpaired_reads #end if $sambam.ignore_umi $sambam.ignore_tlen #if str($sambam.chrom) != '' --chrom '$sambam.chrom' #end if --subset $sambam.subset $sambam.paired ## TODO see comment in LINK_SAM_BAM_INPUT ## #if $input.is_of_type("sam"): ## --in-sam ## #end if $sc.per_gene #if str($sc.gene_tag) != "": --gene-tag '$sc.gene_tag' #end if #if str($sc.assigned_status_tag) != "": --assigned-status-tag '$sc.assigned_status_tag' #end if #if str($sc.skip_tags_regex) != "": --skip-tags-regex '$sc.skip_tags_regex' #end if $sc.per_contig #if $sc.gene_transcript_map: --gene-transcript-map '$sc.gene_transcript_map' #end if $sc.per_cell #if str($advanced.random_seed) != '' --random-seed='$advanced.random_seed' #end if -I '$input_file' -S deduped.bam ## TODO using samtools sort is a workaround, for the following error that appears when Galaxy ## compares the generated file with the one in test-data ## `Converting history BAM to SAM failed: 'samtools returned with error 1: stdout=None, stderr=[main_samview] fail to read the header from "/tmp/tmpd8o61jykdedup_out6.bam".\n'. Will compare BAM files` ## problem seems to be the BAM file generated with pysam ## may be dropped in the future --no-sort-output #if $log: --log='$out_log' #end if --log2stderr && samtools sort --no-PG deduped.bam -@ \${GALAXY_SLOTS:-1} -T "\${TMPDIR:-.}" -o '$output' -O BAM
Functional tests |
name | inputs | outputs | required files |
Test-1 |
input: group_in1.sam bc|extract_umi_method: read_id umi|method: unique advanced|random_seed: 0 |
name: value |
group_in1.sam value |
Test-2 |
input: group_in2.sam bc|extract_umi_method: read_id umi|method: unique sambam|paired: True advanced|random_seed: 0 |
name: value |
group_in2.sam value |
Test-3 |
input: group_in3.bam bc|extract_umi_method: read_id umi|method: unique advanced|random_seed: 0 |
name: value |
group_in3.bam value |
Test-4 |
input: group_in4.bam bc|umi_tag: BX bc|extract_umi_method: tag umi|method: unique advanced|random_seed: 0 |
name: value |
group_in4.bam value |
Test-5 |
input: group_in5.bam bc|extract_umi_method: read_id umi|method: cluster advanced|random_seed: 0 |
name: value |
group_in5.bam value |
Test-6 |
input: group_in6.bam bc|extract_umi_method: read_id umi|method: directional advanced|random_seed: 0 |
name: value |
group_in6.bam value |
Test-7 |
input: group_in6.bam output_stats_bool: True bc|extract_umi_method: read_id umi|method: directional advanced|random_seed: 0 |
name: value |
group_in6.bam value |