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Upgrade mircounts tools #666

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merged 7 commits into from
Feb 10, 2024
Merged

Upgrade mircounts tools #666

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788277c
Upgrade conda packages. IUC format
drosofff Feb 10, 2024
bf1b1b4
lint R, py and xml codes
drosofff Feb 10, 2024
eb58be9
update tests in Mississippi
drosofff Feb 10, 2024
b9485ac
add expect_num_outputs
drosofff Feb 10, 2024
8ab34aa
and ... fix expect_num_outputs="6" (in test tag)
drosofff Feb 10, 2024
1bd51a0
update tests in mississippi
drosofff Feb 10, 2024
646b6c4
reduce test sizes
drosofff Feb 10, 2024
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35 changes: 20 additions & 15 deletions tools/mircounts/coverage_plotting.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,9 +10,10 @@ hlp_output <- "--output\tFILE\tFile to output the pdf to\n"
hlp <- paste(hlp_description, hlp_usage, hlp_dataframe, hlp_type, hlp_output, sep = "\n")

# Setup R error handling to go to stderr
options(show.error.messages = F,
options(show.error.messages = FALSE,
error = function() {
cat(geterrmessage(), file = stderr()); q("no", 1, F)
cat(geterrmessage(), file = stderr())
q("no", 1, FALSE)
}
)

Expand All @@ -26,7 +27,7 @@ option_list <- list(
make_option(c("-t", "--type"), type = "character", default = "relative",
help = "Type of plotting, either relative or absoute coverage values (default = 'relative')"),
make_option(c("-o", "--output"), type = "character", help = "File to output the pdf to")
)
)
parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
args <- parse_args(parser)

Expand All @@ -35,22 +36,26 @@ if (!("dataframe" %in% names(args)) || !("output" %in% names(args))) {
}

# Plot
coverage <- read.delim(args$dataframe, header = T)
coverage <- read.delim(args$dataframe, header = TRUE)
if (args$type == "relative") {
graph <- xyplot(Norm_count ~ Norm_offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
as.table = T, xlab = "Normalized Counts", ylab = "Normalized coordinates",
main = "miRNA coverage maps")
graph <- xyplot(
Norm_count ~ Norm_offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
as.table = TRUE, xlab = "Normalized Counts", ylab = "Normalized coordinates",
main = "miRNA coverage maps"
)
} else {
graph <- xyplot(Count ~ Offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
as.table = T, xlab = "Counts", ylab = "Coordinates",
main = "miRNA coverage plots")
graph <- xyplot(
Count ~ Offset | Mir_hairpin, data = coverage, col = c("darkblue"), type = "l", lwd = 1.5,
scales = list(x = list(cex = .5), y = list(cex = .5)), par.strip.text = list(cex = .5),
strip = strip.custom(which.given = 1, bg = "lightblue"), layout = c(4, 15),
as.table = TRUE, xlab = "Counts", ylab = "Coordinates",
main = "miRNA coverage plots"
)
}

# PDF output
pdf(file = args$output, paper = "special", height = 11.69, width = 8.2677)
plot(graph, newpage = T)
plot(graph, newpage = TRUE)
dev.off()
71 changes: 38 additions & 33 deletions tools/mircounts/mircounts.xml
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@@ -1,42 +1,47 @@
<tool id="mircounts" name="miRcounts" version="1.5.1">
<tool id="mircounts" name="miRcounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<description> Counts miRNA alignments from small RNA sequence data</description>
<macros>
<token name="@TOOL_VERSION@">1.6</token>
<token name="@VERSION_SUFFIX@">0</token>
<token name="@PROFILE@">23.0</token>
</macros>
<requirements>
<requirement type="package" version="1.34=ha1f6473_0">tar</requirement>
<requirement type="package" version="1.3.0=py39h176da8b_2">bowtie</requirement>
<requirement type="package" version="1.12=h9aed4be_1">samtools</requirement>
<requirement type="package" version="0.16.0.1=py39h051187c_3">pysam</requirement>
<requirement type="package" version="1.6.6=r40h6115d3f_1">r-optparse</requirement>
<requirement type="package" version="0.20_44=r40hcfec24a_0">r-lattice</requirement>
<requirement type="package" version="1.34">tar</requirement>
<requirement type="package" version="1.3.1">bowtie</requirement>
<requirement type="package" version="1.19.2">samtools</requirement>
<requirement type="package" version="0.22.0">pysam</requirement>
<requirement type="package" version="1.7.4">r-optparse</requirement>
<requirement type="package" version="0.22_5">r-lattice</requirement>
</requirements>
<stdio>
<exit_code range="1:" level="warning" description="Tool exception" />
</stdio>
<command detect_errors="exit_code"><![CDATA[
tar -xf '$__tool_directory__'/mirbase.tar.gz &&
python '$__tool_directory__'/mature_mir_gff_translation.py
--gff_path mirbase/${mirbase_version}/genomes/${genomeKey}.gff3
--output $gff3 && ## transcode the mature miR genome coordinates into coordinates relative to the corresponding "miRNA_primary_transcript".
--gff_path mirbase/'${mirbase_version}'/genomes/'${genomeKey}'.gff3
--output '$gff3' && ## transcode mature miR genome coordinates relative to "miRNA_primary_transcript"
python '$__tool_directory__'/format_fasta_hairpins.py
--hairpins_path mirbase/${mirbase_version}/hairpin.fa.gz
--basename ${genomeKey}
--hairpins_path mirbase/'${mirbase_version}'/hairpin.fa.gz
--basename '${genomeKey}'
--output hairpin.fa &&
#if $cutadapt.cutoption == "yes":
python '$__tool_directory__'/yac.py --input $cutadapt.input
python '$__tool_directory__'/yac.py --input '$cutadapt.input'
--output clipped_input.fastq
--output_format fastq
--adapter_to_clip $cutadapt.clip_source.clip_sequence
--min $cutadapt.min
--max $cutadapt.max
--Nmode $cutadapt.Nmode &&
--adapter_to_clip '$cutadapt.clip_source.clip_sequence'
--min '$cutadapt.min'
--max '$cutadapt.max'
--Nmode '$cutadapt.Nmode' &&
#else:
ln -f -s '$cutadapt.clipped_input' clipped_input.fastq &&
#end if
bowtie-build hairpin.fa hairpin &&
bowtie -v $v -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '$output' &&
bowtie -v '$v' -M 1 --best --strata --norc -p \${GALAXY_SLOTS:-4} --sam hairpin -q clipped_input.fastq | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o '$output' &&
samtools index $output &&
python '$__tool_directory__'/mircounts.py --alignment $output --gff $gff3 --quality_threshold 10 --pre_mirs $pre_mir_count_file --mirs $mir_count_file --lattice $coverage_dataframe
python '$__tool_directory__'/mircounts.py --alignment '$output' --gff '$gff3' --quality_threshold 10 --pre_mirs '$pre_mir_count_file' --mirs '$mir_count_file' --lattice '$coverage_dataframe'
#if $plotting.plottingOption == 'yes':
&& Rscript '$__tool_directory__'/coverage_plotting.R --dataframe $coverage_dataframe --type $plotting.display --output $latticePDF
&& Rscript '$__tool_directory__'/coverage_plotting.R --dataframe '$coverage_dataframe' --type '$plotting.display' --output '$latticePDF'
#end if
]]></command>
<inputs>
Expand Down Expand Up @@ -135,12 +140,12 @@
</data>
</outputs>
<tests>
<test>
<param name="cutoption" value="no" />
<test expect_num_outputs="6">
<param name="cutoption" value="no"/>
<param name="v" value="1"/>
<param name="genomeKey" value="aga"/>
<param name="mirbase_version" value="22"/>
<param name="clipped_input" value="aga.fastqsanger" ftype="fastqsanger"/>
<param name="clipped_input" value="aga.fastqsanger.gz" ftype="fastqsanger.gz"/>
<param name="plottingOption" value="yes"/>
<param name="display" value="relative"/>
<param name="output_premir_counts" value="True"/>
Expand All @@ -152,8 +157,8 @@
<output name="latticePDF" file="aga_mir_coverage.pdf" ftype="pdf" />
<output name="coverage_dataframe" file="aga_lattice_dataframe.tab" ftype="tabular" />
</test>
<test>
<param name="cutoption" value="yes" />
<test expect_num_outputs="6">
<param name="cutoption" value="yes"/>
<param name="min" value="18"/>
<param name="max" value="32"/>
<param name="Nmode" value="reject"/>
Expand All @@ -173,8 +178,8 @@
<output name="latticePDF" file="mouse_mir_coverage.pdf" ftype="pdf" />
<output name="coverage_dataframe" file="mouse_lattice_dataframe.tab" ftype="tabular" />
</test>
<test>
<param name="cutoption" value="yes" />
<test expect_num_outputs="4">
<param name="cutoption" value="yes"/>
<param name="min" value="15"/>
<param name="max" value="25"/>
<param name="Nmode" value="reject"/>
Expand All @@ -191,8 +196,8 @@
<output name="pre_mir_count_file" file="pre_mirs_unclipped_count.22.tab" ftype="tabular" />
<output name="mir_count_file" file="mirs_unclipped_count.22.tab" ftype="tabular" />
</test>
<test>
<param name="cutoption" value="yes" />
<test expect_num_outputs="4">
<param name="cutoption" value="yes"/>
<param name="min" value="15"/>
<param name="max" value="25"/>
<param name="Nmode" value="reject"/>
Expand All @@ -209,8 +214,8 @@
<output name="pre_mir_count_file" file="pre_mirs_unclipped_count.tab" ftype="tabular" />
<output name="mir_count_file" file="mirs_unclipped_count.tab" ftype="tabular" />
</test>
<test>
<param name="cutoption" value="yes" />
<test expect_num_outputs="6">
<param name="cutoption" value="yes"/>
<param name="min" value="15"/>
<param name="max" value="25"/>
<param name="Nmode" value="reject"/>
Expand All @@ -230,8 +235,8 @@
<output name="latticePDF" file="mir_unclipped_coverage.pdf" ftype="pdf"/>
<output name="coverage_dataframe" file="lattice_unclipped_dataframe.tab" ftype="tabular" />
</test>
<test>
<param name="cutoption" value="no" />
<test expect_num_outputs="6">
<param name="cutoption" value="no"/>
<param name="v" value="1"/>
<param name="genomeKey" value="dme"/>
<param name="mirbase_version" value="21"/>
Expand Down Expand Up @@ -259,7 +264,7 @@

This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments.

.. _mirBase: ftp://mirbase.org/pub/mirbase/
.. _mirBase: https://mirbase.org/download/

------

Expand Down
2 changes: 1 addition & 1 deletion tools/mircounts/test-data/aga.22.gff3
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Expand Up @@ -11,7 +11,7 @@
# rather a predicted stem-loop portion that includes the precursor
# miRNA. Mature sequences have type "miRNA".
#
# generated by mature_mir_gff_translation.py 2021-05-09 00:34:02.737449
# generated by mature_mir_gff_translation.py 2024-02-10 17:38:20.268084
#
aga-bantam . miRNA_primary_transcript 1 111 . + . ID=MI0001599;Alias=MI0001599;Name=aga-bantam
aga-bantam . miRNA 70 92 . + . ID=MIMAT0001494;Alias=MIMAT0001494;Name=aga-bantam;Derives_from=MI0001599;Parent_mir_Name=aga-bantam
Expand Down
Binary file modified tools/mircounts/test-data/aga.bam
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