Mercurial > repos > iuc > umi_tools_count
diff umi-tools_counts.xml @ 0:8db56d2f8b72 draft
planemo upload commit c79a5f4a05156bb2a6035a844aa9ad8f0e59ecb5
| author | iuc |
|---|---|
| date | Thu, 21 Jun 2018 15:20:14 -0400 |
| parents | |
| children | 3c932ad4a174 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/umi-tools_counts.xml Thu Jun 21 15:20:14 2018 -0400 @@ -0,0 +1,188 @@ +<tool id="umi_tools_count" name="UMI-tools count" version="@VERSION@.0"> + <description>Count UMIs from BAM files</description> + <macros> + <import>macros.xml</import> + <xml name="sanitize_tag" > + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits" /> + </sanitizer> + </xml> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + ln -s '${input_bam}' 'input.bam' && + ln -s '${input_bam.metadata.bam_index}' 'input.bam.bai' && + + umi_tools count + -I input.bam + '$bam_paired' + --extract-umi-method='$barcodes.extract_umi_method.value' + #if $barcodes.extract_umi_method == 'read_id': + --umi-separator='$barcodes.delimiter' + #else if $barcodes.extract_umi_method == 'tag': + --umi-tag='$barcodes.umi_tag' + --cell-tag='$barcodes.cell_tag' + #end if + --method='$grouping_method.value' + --edit-distance-threshold='$hamming_distance' + --mapping-quality='$advanced.mapping_quality' + --per-gene + $wide_format_cell_counts + $advanced.per_contig + '$advanced.per_cell' + #if $advanced.gene_tag: + --gene-tag='$advanced.gene_tag' + #end if + #if $advanced.skip_tags_regex.value: + --skip-tags-regex='$advanced.skip_tags_regex' + #end if + #if $advanced.random_seed != 0: + --random-seed='$advanced.random_seed' + #end if + -S '$out_counts' + -L '$out_log' + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" label="Sorted BAM file" help="Please use the samtools sort tool to ensure a correct BAM input" /> + + <param name="bam_paired" type="boolean" truevalue="--paired" falsevalue="" checked="false" + label="Bam is paired-end" + help="both read pairs will be output. This will also force the use of the template length to determine +reads with the same mapping coordinates." /> + + <conditional name="barcodes" > + <param name="extract_umi_method" type="select" label="Umi Extract Method" help="How are the barcodes encoded in the read?" > + <option value="read_id" selected="true">Barcodes are contained at the end of the read seperated by a delimiter</option> + <option value="tag" >Barcodes are contained in tags</option> + <option value="umis" >Barcodes were extracted using umis</option> + </param> + <when value="read_id" > + <param name="delimiter" type="text" label="Delimiter between read id and the UMI" value="_" > + <expand macro="sanitize_tag" /> + </param> + </when> + <when value="tag" > + <param name="umi_tag" type="text" label="Tag which contains the UMI" > + <expand macro="sanitize_tag" /> + </param> + <param name="cell_tag" type="text" label="Tag which contains the cell barcode" > + <expand macro="sanitize_tag" /> + </param> + </when> + <when value="umis"></when> + </conditional> + + <param name="grouping_method" type="select" label="Method to identify group of reads" help="UMIs with the same (or similar) codes can be grouped together. The simplest methods 'unique' and 'percentile' group identical +UMIs, however 'cluster', 'adjacency', and 'directional' can group similar umis with edit distances less than some threshold. Unique: Reads group share the exact same UMI. Percentile: Reads group share the same UMI, and UMIs with +counts < 1% of the median counts for UMIs at the same position are ignored. Cluster: Identify clusters of connected UMIs (based on hamming distance threshold). Adjacency: Same as cluster, but considers only directly ajacent +UMIs in the cluster. Directional: Identify cluster of connected UMIs based on hamming distance and umi." > + <option value="unique" >Unique</option> + <option value="percentile">Percentile</option> + <option value="cluster">Cluster</option> + <option value="adjacency">Adjacency</option> + <option value="directional" selected="true" >Directional</option> + </param> + + <param name="hamming_distance" type="integer" label="Edit distance threshold" min="0" value="1" /> + <param name="wide_format_cell_counts" type="boolean" truevalue="--wide-format-cell-counts" falsevalue="" checked="false" label="Output a mtrix of genes and cells, instead of a flat file" /> + + <section name="advanced" title="Extra parameters" > + <param name="mapping_quality" type="integer" min="0" value="0" label="Minimum mapping quality" /> + <!-- Currently hard-coded parameter. Leave here if useful to future wrapper --> + <!-- <param argument="-\-per-gene" name="per_gene" type="text" label="Group reads together if they have the same gene" help="Reads will be grouped together if they have the same gene. This is useful if your library +prep generates PCR duplicates with non-identical alignment positions such as CEL-Seq. Note this option is hardcoded to be on with the count command. I.e counting is always performed per-gene. Must be combined with either +-\-gene-tag or -\-per-contig option" /> --> + <param name="gene_tag" type="text" label="Deduplicate per gene." help="The gene information is encoded in the bam read tag." value="" > + <expand macro="sanitize_tag" /> + </param> + <param name="skip_tags_regex" type="text" label="Skip any reads where the gene matches this tag" value="" > + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"> + <add value="!="/> + <add value="-"/> + <add value="_"/> + <add value="."/> + <add value="?"/> + <add value="<"/><!-- left triangle bracket --> + <add value=">"/><!-- right triangle bracket --> + <add value="["/> <!-- left square bracket --> + <add value="]"/> <!-- right square bracket --> + <add value="^"/> <!-- caret --> + <add value="{"/> <!-- left curly --> + <add value="}"/> <!-- right curly --> + <add value="("/> <!-- left parenthesis --> + <add value=")"/> <!-- right parenthesis --> + </valid> + </sanitizer> + </param> + <param name="per_contig" type="boolean" truevalue="--per-contig" falsevalue="" checked="false" + label="Deduplicate per contig (field 3 in BAM; RNAME)" + help="All reads with the same contig will be considered to have the same alignment position. This is useful if you have aligned to a reference transcriptome with one transcript per gene." /> + <param name="per_cell" type="boolean" truevalue="--per-cell" falsevalue="" checked="false" + label="Group reads only if they have the same cell barcode." /> + <param name="random_seed" type="integer" min="0" value="0" label="Random Seed" /> + </section> + </inputs> + <outputs> + <data name="out_counts" format="tsv" /> + <data name="out_log" format="txt" /> + </outputs> + <tests> + <test><!--count_single_gene_tag:--> + <param name="input_bam" value="chr19_gene_tags.bam" /> + <param name="random_seed" value="123456789" /> + <param name="grouping_method" value="directional" /> + <param name="gene_tag" value="XF" /> + <param name="skip_tags_regex" value="^[__|Unassigned]" /> + <param name="extract_umi_method" value="umis" /> + <output name="out_counts" value="count_single_gene_tag.tsv" /> + </test> + <test><!--count_single_cells_gene_tag:--> + <param name="input_bam" value="chr19_gene_tags.bam" /> + <param name="random_seed" value="123456789" /> + <param name="grouping_method" value="directional" /> + <param name="gene_tag" value="XF" /> + <param name="skip_tags_regex" value="^[__|Unassigned]" /> + <param name="per_cell" value="true" /><!-- new --> + <param name="extract_umi_method" value="umis" /> + <output name="out_counts" value="count_single_cells_gene_tag.tsv" /> + </test> + <test><!--count_single_cells_wide_gene_tag:--> + <param name="input_bam" value="chr19_gene_tags.bam" /> + <param name="random_seed" value="123456789" /> + <param name="grouping_method" value="directional" /> + <param name="gene_tag" value="XF" /> + <param name="skip_tags_regex" value="^[__|Unassigned]" /> + <param name="per_cell" value="true" /><!-- new --> + <param name="extract_umi_method" value="umis" /> + <param name="wide_format_cell_counts" value="true" /> + <output name="out_counts" value="count_single_cells_gene_tag_wide.tsv" /> + </test> + </tests> + <help><![CDATA[ + +UMI Tools count - Count reads per gene from BAM using UMIs +---------------------------------------------------------- + +Purpose +------- + +The purpose of this command is to count the number of reads per gene based +on the mapping co-ordinate and the UMI attached to the read. + + +It is assumed that the FASTQ files were processed with extract_umi.py +before mapping and thus the UMI is the last word of the read name. e.g: + +@HISEQ:87:00000000_AATT + +where AATT is the UMI sequeuence. + +If you have used an alternative method which does not separate the +read id and UMI with a "_", such as bcl2fastq which uses ":", you can +specify the separator, or if your UMIs are encoded in a tag you can also specify this. + + ]]></help> + <expand macro="citations" /> +</tool>