Mercurial > repos > iuc > sinto_barcode
changeset 0:3780db0073f0 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sinto commit a836e4e010093207186d4d7839bbba702a15c18f
| author | iuc |
|---|---|
| date | Thu, 13 Apr 2023 11:03:48 +0000 |
| parents | |
| children | d1b34ac42b8f |
| files | macros.xml sinto_barcode.xml test-data/aligned.bam test-data/barcodes.fastq.gz test-data/read1.barcoded.fastq.gz test-data/read1.fastq.gz test-data/read2.barcoded.fastq.gz test-data/read2.fastq.gz |
| diffstat | 6 files changed, 88 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Apr 13 11:03:48 2023 +0000 @@ -0,0 +1,11 @@ +<?xml version="1.0"?> +<macros> + <token name="@TOOL_VERSION@">0.9.0</token> + <token name="@VERSION_SUFFIX@">0</token> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/s41592-021-01282-5</citation> + </citations> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sinto_barcode.xml Thu Apr 13 11:03:48 2023 +0000 @@ -0,0 +1,77 @@ +<tool id="sinto_barcode" name="Sinto barcode" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> + <description>add cell barcodes to FASTQ read names</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <requirement type="package" version="@TOOL_VERSION@">sinto</requirement> + </requirements> + <version_command>sinto --version</version_command> + <command><![CDATA[ + ln -s '$barcode_fastq' barcodes.fastq.gz && + ln -s '${fastq_input.read1_fastq}' read1.fastq.gz && + #if str( $fastq_input.fastq_input_selector ) == "paired": + ln -s '${fastq_input.read2_fastq}' read2.fastq.gz && + #end if + sinto barcode + --barcode_fastq barcodes.fastq.gz + --read1 read1.fastq.gz + #if str( $fastq_input.fastq_input_selector ) == "paired": + --read2 read2.fastq.gz + #end if + --bases $bases +]]> </command> + <inputs> + <param type="data" name="barcode_fastq" format="fastqsanger.gz" label="FASTQ file containing cell barcode sequences" /> + <conditional name="fastq_input"> + <param name="fastq_input_selector" type="select" label="Single or Paired-end data"> + <option value="paired">Paired</option> + <option value="single">Single</option> + </param> + <when value="paired"> + <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Forward reads FASTQ file" /> + <param name="read2_fastq" type="data" format="fastqsanger.gz" label="Reverse reads FASTQ file" /> + </when> + <when value="single"> + <param name="read1_fastq" type="data" format="fastqsanger.gz" label="Select FASTQ file" /> + </when> + </conditional> + <param type="integer" name="bases" value="16" min="0" label="Number of bases to extract from barcode-containing FASTQ" /> + </inputs> + <outputs> + <data name='read1_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 1" from_work_dir="read1.barcoded.fastq" /> + <data name='read2_out' format='fastqsanger.gz' label="${tool.name} on ${on_string}: barcoded read 2" from_work_dir="read2.barcoded.fastq" > + <filter>fastq_input['fastq_input_selector'] == 'paired'</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="barcode_fastq" value="barcodes.fastq.gz" /> + <param name="fastq_input_selector" value="single"/> + <param name="read1_fastq" value="read1.fastq.gz" /> + <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> + </test> + <test expect_num_outputs="2"> + <param name="barcode_fastq" value="barcodes.fastq.gz" /> + <param name="fastq_input_selector" value="paired"/> + <param name="read1_fastq" value="read1.fastq.gz" /> + <param name="read2_fastq" value="read2.fastq.gz" /> + <output name="read1_out" file="read1.barcoded.fastq.gz" ftype="fastqsanger.gz" decompress="true"/> + <output name="read2_out" file="read2.barcoded.fastq.gz" ftype="fastqsanger.gz" decompress="true"/> + </test> + </tests> + <help><![CDATA[ + +Sinto is a toolkit for processing aligned single-cell data. +-------------------------------------------------------------------------------------------------------------- +Cell barcodes from one FASTQ file added to the read names of another, or the same, FASTQ file. This is useful when processing raw single-cell sequencing data, as the cell barcode information can easily be propagated to the aligned BAM file by encoding the cell barcode in the read name. + +**Inputs** +FASTQ files containing barcodes and forward reads. An optional reverse reads FASTQ file can be provided for paired-end experiments. Note that all the FASTQs must contain the same number of reads and the reads must appear in the same order. + +**Outputs** +FASTQ files with the read names modified to contain the cell barcode sequence at the beginning of the read name, separated from the original read name by a : character. + + ]]> </help> + <expand macro="citations" /> +</tool>