Mercurial > repos > peterjc > fastq_filter_by_id
view tools/fastq/fastq_filter_by_id.xml~ @ 2:d570cc324779
Migrated tool version 0.0.4 from old tool shed archive to new tool shed repository
author | peterjc |
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date | Tue, 07 Jun 2011 17:24:08 -0400 |
parents | b79caa511ba2 |
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<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.2"> <description>from a tabular file</description> <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="fastq" label="With matched ID"> <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> <change_format> <when input_dataset="input_fastq" attribute="extension" value="fastqsanger" format="fastqsanger" /> <when input_dataset="input_fastq" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> <when input_dataset="input_fastq" attribute="extension" value="fastqillumina" format="fastqillumina" /> <when input_dataset="input_fastq" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> </change_format> <filter>output_choice_cond["output_choice"] != "neg"</filter> </data> <data name="output_neg" format="fastq" label="Without matched ID"> <!-- TODO - Replace this with format="input:input_fastq" if/when that works --> <change_format> <when input_dataset="input_fastq" attribute="extension" value="fastqsanger" format="fastqsanger" /> <when input_dataset="input_fastq" attribute="extension" value="fastqsolexa" format="fastqsolexa" /> <when input_dataset="input_fastq" attribute="extension" value="fastqillumina" format="fastqillumina" /> <when input_dataset="input_fastq" attribute="extension" value="fastqcssanger" format="fastqcssanger" /> </change_format> <filter>output_choice_cond["output_choice"] != "pos"</filter> </data> </outputs> <tests> </tests> <help> **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> </tool>