Mercurial > repos > peterjc > fastq_filter_by_id
view tools/fastq_filter_by_id/fastq_filter_by_id.xml @ 3:e0041942a12d draft default tip
v0.0.5 - galaxy_sequence_utils dependency and other cleanups inc using MIT license
author | peterjc |
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date | Fri, 03 Feb 2017 05:34:18 -0500 |
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<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.5" hidden="true"> <description>from a tabular file</description> <requirements> <requirement type="package" version="1.0.1">galaxy_sequence_utils</requirement> </requirements> <version_command interpreter="python">fastq_filter_by_id.py --version</version_command> <command interpreter="python"> fastq_filter_by_id.py $input_tabular $columns $input_fastq #if $output_choice_cond.output_choice=="both" $output_pos $output_neg #elif $output_choice_cond.output_choice=="pos" $output_pos - #elif $output_choice_cond.output_choice=="neg" - $output_neg #end if </command> <inputs> <param name="input_fastq" type="data" format="fastq" label="FASTQ file to filter on the identifiers"/> <param name="input_tabular" type="data" format="tabular" label="Tabular file containing FASTQ identifiers"/> <param name="columns" type="data_column" data_ref="input_tabular" multiple="True" numerical="False" label="Column(s) containing FASTA identifiers" help="Multi-select list - hold the appropriate key while clicking to select multiple columns"> <validator type="no_options" message="Pick at least one column"/> </param> <conditional name="output_choice_cond"> <param name="output_choice" type="select" label="Output positive matches, negative matches, or both?"> <option value="both">Both positive matches (ID on list) and negative matches (ID not on list), as two FASTA files</option> <option value="pos">Just positive matches (ID on list), as a single FASTA file</option> <option value="neg">Just negative matches (ID not on list), as a single FASTA 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> </inputs> <outputs> <data name="output_pos" format_source="input_fastq" metadata_source="input_fastq" label="With matched ID"> <filter>output_choice_cond["output_choice"] != "neg"</filter> </data> <data name="output_neg" format_source="input_fastq" metadata_source="input_fastq" label="Without matched ID"> <filter>output_choice_cond["output_choice"] != "pos"</filter> </data> </outputs> <tests> <test> <param name="input_fastq" value="sanger-pairs-mixed.fastq" ftype="fastq" /> <param name="input_tabular" value="sanger-pairs-names.tabular" ftype="tabular" /> <param name="columns" value="1" /> <param name="output_choice" value="both" /> <output name="output_pos" file="empty_file.dat" ftype="fastq" /> <output name="output_neg" file="sanger-pairs-mixed.fastq" ftype="fastq" /> </test> </tests> <help> **Deprecated** This tool is now obsolete, and should not be used in future. It has been replaced by a more general version covering FASTA, FASTQ and SFF in one single tool. **What it does** By default it divides a FASTQ file in two, those sequences with or without an ID present in the tabular file column(s) specified. You can opt to have a single output file of just the matching records, or just the non-matching ones. Note that the order of sequences in the original FASTA file is preserved. Also, if any sequences share an identifier, duplicates are not removed. **Example Usage** You may have performed some kind of contamination search, for example running BLASTN against a database of cloning vectors or bacteria, giving you a tabular file containing read identifiers. You could use this tool to extract only the reads without BLAST matches (i.e. those which do not match your contaminant database). </help> <citations> <citation type="doi">10.7717/peerj.167</citation> </citations> </tool>