Mercurial > repos > peterjc > seq_filter_by_mapping
view tools/seq_filter_by_mapping/seq_filter_by_mapping.xml @ 6:566e456371c6 draft default tip
Drop biopython from tool_dependencies.xml
author | peterjc |
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date | Thu, 30 Nov 2023 10:12:54 +0000 |
parents | 1d6c149ca211 |
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<tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.8"> <description>from SAM/BAM file</description> <requirements> <requirement type="package" version="1.81">biopython</requirement> <requirement type="package" version="0.1.19">samtools</requirement> </requirements> <version_command> python $__tool_directory__/seq_filter_by_mapping.py --version </version_command> <command detect_errors="aggressive"> python $__tool_directory__/seq_filter_by_mapping.py -i '$input_file' -f '$input_file.ext' -m $pair_mode #if $output_choice_cond.output_choice=="both" -p '$output_pos' -n '$output_neg' #elif $output_choice_cond.output_choice=="pos" -p '$output_pos' #elif $output_choice_cond.output_choice=="neg" -n '$output_neg' #end if ## Now loop over all the mapping files #for i in $mapping_file#'${i}' #end for# </command> <inputs> <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." /> <param name="mapping_file" type="data" format="sam,bam" multiple="true" label="SAM/BAM mapping of those sequences" help="SAM or BAM format." /> <conditional name="output_choice_cond"> <param name="output_choice" type="select" label="Output mapped reads, unmapped reads, or both?"> <option value="both">Both mapped and unmapped reads, as two files</option> <option value="pos">Just mapped reads, as a single file</option> <option value="neg">Just unmapped reads, as a single file</option> </param> <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml --> <when value="both" /> <when value="pos" /> <when value="neg" /> </conditional> <param name="pair_mode" type="select" label="Paired read treatment"> <option value="lax" selected="true">Treat as a pair, allow either read to be mapped</option> <option value="strict">Treat as a pair, require both reads to be mapped</option> <!-- The following would actually be more work as have to store qname/1 and qname/2 separately for filter... <option value="solo">Treat independently (will split partners when only one maps)</option> --> </param> </inputs> <outputs> <data name="output_pos" format_source="input_file" metadata_source="input_file" label="$input_file.name (mapped)"> <filter>output_choice_cond["output_choice"] != "neg"</filter> </data> <data name="output_neg" format_source="input_file" metadata_source="input_file" label="$input_file.name (unmapped)"> <filter>output_choice_cond["output_choice"] != "pos"</filter> </data> </outputs> <tests> <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="lax" /> <param name="output_choice" value="pos" /> <output name="output_pos" file="SRR639755_sample_lax.fastq" ftype="fastqsanger" /> </test> <test> <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" /> <param name="pair_mode" value="strict" /> <param name="output_choice" value="pos" /> <output name="output_pos" file="SRR639755_sample_strict.fastq" ftype="fastqsanger" /> </test> </tests> <help> **What it does** By default it divides a FASTA, FASTQ or Standard Flowgram Format (SFF) file in two, those sequences (or read pairs) which do or don't map in the provided SAM/BAM file. You can opt to have a single output file of just the mapping reads, or just the non-mapping ones. **Example Usage** You might wish to perform a contamination screan by mapping your reads against known contaminant reference sequences, then use this tool to select only the unmapped reads for further analysis (e.g. *de novo* assembly). Similarly you might wish to map your reads against a known bacterial reference, then take the non-mapping sequences forward for analysis if looking for novel plasmids. **References** If you use this Galaxy tool in work leading to a scientific publication please cite: Peter J.A. Cock (2014), Galaxy tool for filtering reads by mapping http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping This tool uses Biopython to read and write SFF files, so you may also wish to cite the Biopython application note (and Galaxy too of course): Cock et al (2009). Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3. https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878. This tool is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping </help> <citations> <citation type="doi">10.1093/bioinformatics/btp163</citation> </citations> </tool>