[WIP] Add fastq_util tool fastq_pre_barcodes to qc dir #252
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| <tool id="fastq_pre_barcodes" name="FASTQ barcodes preprocessor" profile="10" version="conda-package-version+galaxy0"> | ||
| <description>Preprocesses the reads to move the barcodes (UMI, Cell, ...) to the respective readname, optionally discarding reads with bases in the barcode regions below a given threshold.</description> | ||
| <command detect_errors="exit_code"><![CDATA[ | ||
| #set params_optional = [] | ||
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| #if $read2: | ||
| ${params_optional}.append($read2) | ||
| #end if | ||
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| #if $index1: | ||
| ${params_optional}.append($index1) | ||
| #end if | ||
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| #if $index2: | ||
| ${params_optional}.append($index2) | ||
| #end if | ||
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| #if $index3: | ||
| ${params_optional}.append($index3) | ||
| #end if | ||
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| #if $phred_encoding: | ||
| ${params_optional}.append($phred_encoding) | ||
| #end if | ||
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| #if $min_qual: | ||
| ${params_optional}.append($min_qual) | ||
| #end if | ||
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| #if $outfile2: | ||
| ${params_optional}.append($outfile2) | ||
| #end if | ||
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| #if $outfile3: | ||
| ${params_optional}.append($outfile3) | ||
| #end if | ||
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| #if $interleaved: | ||
| ${params_optional}.append($interleaved) | ||
| #end if | ||
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| #if $umi_read: | ||
| ${params_optional}.append($umi_read) | ||
| #end if | ||
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| #if $umi_offset: | ||
| ${params_optional}.append($umi_offset) | ||
| #end if | ||
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| #if $umi_size: | ||
| ${params_optional}.append($umi_size) | ||
| #end if | ||
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| #if $Cell_read: | ||
| ${params_optional}.append($Cell_read) | ||
| #end if | ||
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| #if $Cell_offset: | ||
| ${params_optional}.append($Cell_offset) | ||
| #end if | ||
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| #if $Cell_size: | ||
| ${params_optional}.append($Cell_size) | ||
| #end if | ||
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| #if $sample_read: | ||
| ${params_optional}.append($sample_read) | ||
| #end if | ||
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| #if $sample_offset: | ||
| ${params_optional}.append($sample_offset) | ||
| #end if | ||
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| #if $sample_size: | ||
| ${params_optional}.append($sample_size) | ||
| #end if | ||
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| #if $read1_offset: | ||
| ${params_optional}.append($read1_offset) | ||
| #end if | ||
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| #if $read1_size: | ||
| ${params_optional}.append($read1_size) | ||
| #end if | ||
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| #if $read2_offset: | ||
| ${params_optional}.append($read2_offset) | ||
| #end if | ||
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| #if $read2_offset: | ||
| ${params_optional}.append($read2_offset) | ||
| #end if | ||
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| #if $use_10x: | ||
| ${params_optional}.append($use_10x) | ||
| #end if | ||
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| #if $brief: | ||
| ${params_optional}.append($brief) | ||
| #elif $verbose: | ||
| ${params_optional}.append($verbose) | ||
| #end if | ||
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| # set params_optional_str = " ".join($params_optional) | ||
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| fastq_pre_barcodes --read1 $read1 --outfile $outfile1 $params_optional_str | ||
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| ]]></command> | ||
| <inputs> | ||
| <param label="Verbose" optional='true' value='false' name="verbose" argument="--verbose" type="boolean" truevalue='--verbose' falsevalue='' checked='true' help="Increase level of messages printed to stderr"/> | ||
| <param label="Brief" optional='true' value='true' name="brief" argument="--brief" type="boolean" truevalue='--brief' falsevalue='' checked='true' help="Decrease level of messages printed to stderr"/> | ||
| <param label="Read1" name="read1" argument="--read1" type="data" format='?' help="fastq (optional gzipped) file name"/> | ||
| <param label="Read2" name="read2" argument="--read2" type="data" format='?' help="fastq (optional gzipped) file name"/> | ||
| <param label="Index1" name="index1" argument="--index1" type="data" format='?' help="fastq (optional gzipped) file name"/> | ||
| <param label="Index2" name="index2" argument="--index2" type="data" format='?' help="fastq (optional gzipped) file name"/> | ||
| <param label="Index3" name="index3" argument="--index3" type="data" format='?' help="fastq (optional gzipped) file name"/> | ||
| <param label="PHRED Encoding" name="phred_encoding" argument="--phred_encoding" type="select" help="PHRED encoding used in the input files"> | ||
| <option value="33" selected="true">33</option> | ||
| <option value="64">64</option> | ||
| </param> | ||
| <param label="Minimum Quality" optional='true' value='' name="min_qual" argument="--min_qual" type="integer" min="0" max="40" help="[0-40]. Defines the minimum quality that all bases in the UMI, Cell or Sample should have (reads that do not pass the criteria are discarded). 0 disables the filter."/> | ||
| <param label="Interleaved Data" name="interleaved" argument="--interleaved" type="text" help="Interleaved data, in this format: (read1|read2|index1|index2|index3),(read1|read2|index1|index2|index3)"/> | ||
| <param label="UMI read" name="umi_read" argument="--umi_read" type="text" help="File in which UMI read can be found, in this format: (read1|read2|index1|index2|index3)"/> | ||
| <param label="UMI offset" name="umi_offset" argument="--umi_offset" type="integer" help="Offset (integer)"/> | ||
| <param label="UMI Size" name="umi_size" argument="--umi_size" type="integer" help="Number of bases after the offset"/> | ||
| <param label="Cell Read" name="Cell_read" argument="--Cell_read" type="text" help="File in which Cell can be found, in this format: (read1|read2|index1|index2|index3)"/> | ||
| <param label="Cell Offset" name="Cell_offset" argument="--Cell_offset" type="integer" help="Offset"/> | ||
| <param label="Cell Size" name="Cell_size" argument="--Cell_size" type="integer" help="Number of bases after the offset"/> | ||
| <param label="Sample Read" name="sample_read" argument="--sample_read" type="text" help="File in which sample barcode can be found, in this format: (read1|read2|index1|index2|index3)"/> | ||
| <param label="Sample Offset" name="sample_offset" argument="--sample_offset" type="integer" help="Offset"/> | ||
| <param label="Sample Size" name="sample_size" argument="--sample_size" type="integer" help="Number of bases after the offset"/> | ||
| <param label="read1 Offset" name="read1_offset" argument="--read1_offset" type="integer" help="None"/> | ||
| <param label="read1 Size" name="read1_size" argument="--read1_size" type="integer" help="None"/> | ||
| <param label="read2 Offset" name="read2_offset" argument="--read2_offset" type="integer" help="None"/> | ||
| <param label="read2 Size" name="read2_size" argument="--read2_size" type="integer" help="None"/> | ||
| <param label="Use 10x tags" name="use_10x" argument="--10x" type="text" help="Use 10X UMI tags (UB and UY) instead of the default tags defined in the SAM specification"/> | ||
| </inputs> | ||
| <outputs> | ||
| <data label="${tool.name} on ${on_string}: Output file 1" name="outfile1" format='?' /> | ||
| <data label="${tool.name} on ${on_string}: Output file 2" name="outfile2" format='?' /> | ||
| <data label="${tool.name} on ${on_string}: Output file 3" name="outfile3" format='?' /> | ||
|
There was a problem hiding this comment. also format needs to be set here, please see galaxy datatypes in the Galaxy docs. There was a problem hiding this comment. Done in 3896d3d. |
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| </outputs> | ||
| <tests></tests> | ||
| <help></help> | ||
| </tool> | ||
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Missing the requirements as well (the bioconda package that this will use to run)
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Done in 51b56db but I'm not sure if I referenced the correct version for samtools.
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I suspect that that will be hard to know, @pinin4fjords might be able to point you to where IRAP is installed on Noah to check the version used. We could in principle try a few runs with this (I suspect most up to date) version and if results are equivalent maybe we keep the newest version. Although maybe for a start, might be better to go if possible with the currently used version in noah.
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I tried here: https://wwwdev.ebi.ac.uk/gxa/experiments/E-MTAB-2706/Supplementary%20Information but it is not mentioned.
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irap has samtools samtools 1.9, fastq_utils 0.16.3
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Changed in 3896d3d, but the test log says it's still using fastq_utils 0.25.1. Any idea how I might force it to use the correct fastq_utils version?
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I'm not seeing what you mean in the logs right now, but it may be because that version isn't available in Conda- see https://anaconda.org/bioconda/fastq_utils/files. You could try picking the oldest version available for now, but since we can't easily match versions maybe we should bite the bullet and use the latest. Okay with you @pcm32 ?
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The html output of the local planemo test that I ran says
fastq_utils 0.25.1in its report. Not sure how to view the html here, but maybe they're using the same version.According to the fastq_utils repo, these are the dependencies:
samtools (version 0.1.19) and zlib (http://zlib.net/) version 1.2.11 or latest are required to compile fastq_utils. ... The bam_annotate.sh script requires samtools (version 1.5 or higher).There was a problem hiding this comment.
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Changed to latest version in c40fc6a