Mercurial > repos > peterjc > fastq_filter_by_id
changeset 1:b79caa511ba2
Migrated tool version 0.0.3 from old tool shed archive to new tool shed repository
| author | peterjc |
|---|---|
| date | Tue, 07 Jun 2011 17:23:49 -0400 |
| parents | 10e963c79a45 |
| children | d570cc324779 |
| files | tools/fastq/fastq_filter_by_id.xml tools/fastq/fastq_filter_by_id.xml~ |
| diffstat | 2 files changed, 80 insertions(+), 7 deletions(-) [+] |
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--- a/tools/fastq/fastq_filter_by_id.xml Tue Jun 07 17:23:26 2011 -0400 +++ b/tools/fastq/fastq_filter_by_id.xml Tue Jun 07 17:23:49 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.2"> +<tool id="fastq_filter_by_id" name="Filter FASTQ by ID" version="0.0.3"> <description>from a tabular file</description> <command interpreter="python"> fastq_filter_by_id.py $input_tabular $columns $input_fastq @@ -60,16 +60,14 @@ 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. +Note that the order of sequences in the original FASTQ 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). +You may have mapped your reads against a reference genome, and thus generated +a tabular file of the mapped reads. You could use this tool to divide the reads +into those which map onto the genome, and those which don't. </help> </tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/fastq/fastq_filter_by_id.xml~ Tue Jun 07 17:23:49 2011 -0400 @@ -0,0 +1,75 @@ +<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>