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changeset 0:53440b7599a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp/ commit 31eda859c4e23cd76d1e30824cc6899e8fc1e16a
author iuc
date Wed, 21 May 2025 21:08:34 +0000
parents
children d4f671d70a65
files nanocomp.xml test-data/in1.fastq.gz test-data/in2.fastq.gz test-data/in3.fastq.gz test-data/in4.bam test-data/in5.bam
diffstat 6 files changed, 258 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanocomp.xml	Wed May 21 21:08:34 2025 +0000
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+<tool id="nanocomp" name="NanoComp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
+	<description>Compare multiple runs of long read sequencing data and alignments.</description>
+	<macros>
+		<token name="@TOOL_VERSION@">1.25.2</token>
+		<token name="@VERSION_SUFFIX@">0</token>
+	</macros>
+	<xrefs>
+		<xref type="bio.tools">nanocomp</xref>
+	</xrefs>
+		<requirements>
+			<requirement type="package" version="@TOOL_VERSION@">nanocomp</requirement>
+		</requirements>
+	<version_command>NanoComp -v</version_command>
+	<command detect_errors="exit_code"><![CDATA[
+ #import re
+ ##link input file with names
+  #for $file in $inputs.input_type.input_data
+   #if '.' in str($file.name)
+    #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))
+   #else
+    #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))  + "." + $file.ext
+   #end if
+   ln -sf $file $in_name &&
+  #end for
+
+ ##run nanocomp
+  NanoComp
+
+  ##no need for the static images (becomes deprecated)
+  --make_no_static
+
+ ## Compute options
+  --threads \${GALAXY_SLOTS:-4}
+
+ ##add input files
+  #if $inputs.input_type.input_type_selector == "fastq"
+   --fastq
+  #else if $inputs.input_type.input_type_selector == "fastq_r" 
+   --fastq_rich
+  #else if $inputs.input_type.input_type_selector == "fasta"
+   --fasta
+  #else if $inputs.input_type.input_type_selector == "bam"
+   --bam
+  #else if $inputs.input_type.input_type_selector == "ubam"
+   --ubam
+  #else if $inputs.input_type.input_type_selector == "cram"
+   --cram
+  #else if $inputs.input_type.input_type_selector == "pickle"
+   --pickle
+  #else if $inputs.input_type.input_type_selector == "arrow"
+   --arrow
+  #end if
+
+  #for $file in $inputs.input_type.input_data
+   #if '.' in str($file.name)
+    #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))
+   #else
+    #set $in_name = re.sub('[\-\:\s]', '_', str($file.name))  + "." + $file.ext
+   #end if
+   $in_name
+  #end for
+
+ ##Filter options
+  #if $filters.maxlength
+    --maxlength $filters.maxlength
+  #end if
+  #if $filters.minlength
+    --minlength $filters.minlength
+  #end if
+
+ ##Plot options
+  #if $plot_options.plot
+    --plot $plot_options.plot 
+  #end if
+
+  #if $plot_options.title
+    --title "$plot_options.title"
+  #end if
+
+  #if $plot_options.names
+    --names $plot_options.names
+  #end if
+
+  #if $plot_options.colors
+    --colors $plot_options.colors
+  #end if
+
+ ##Output options
+  #if $output_options.tsv_stats
+    $output_options.tsv_stats
+  #end if
+
+  --verbose 
+  >& $out_log
+
+]]></command>
+	<inputs>
+		<section name="inputs" title="Input data" expanded="True"> 
+			<conditional name="input_type">
+				<param name="input_type_selector" type="select" label="Choose Input Format and Files">
+					<option value="fastq" selected="true">FASTQ files</option>
+					<option value="fastq_r">FASTQ-rich files</option>
+					<option value="fasta">FASTA files</option>
+					<option value="bam">BAM files</option>
+					<option value="ubam">uBAM files</option>
+					<option value="cram">CRAM files</option>
+					<option value="pickle">PICKLE files</option>
+					<option value="arrow">ARROW files</option>
+				</param>
+				<when value="fastq">
+					<param name="input_data" type="data" format="fastq,fastq.gz" multiple="true" label="FASTQ input files" help="Data is in (compressed) fastq format" />
+				</when>
+				<when value="fastq_r">
+					<param name="input_data" type="data" format="fastq,fastq.gz" multiple="true" label="FASTQ input files" help="Data is in one or more fastq file(s) generated by MinKNOW or guppy with additional information concerning channel and time" />
+				</when>
+				<when value="fasta">
+					<param name="input_data" type="data" format="fasta,fasta.gz" multiple="true" label="FASTA input files" help="Data is in (compressed) fasta format" />
+				</when>
+				<when value="bam">
+					<param name="input_data" type="data" format="bam" multiple="true" label="BAM input files" help="Data is in sorted bam files." />
+				</when>
+				<when value="ubam">
+					<param name="input_data" type="data" format="bam" multiple="true" label="Unmapped BAM input files" help="Data is in one or more unmapped bam files." />
+				</when>
+				<when value="cram">
+					<param name="input_data" type="data" format="cram" multiple="true" label="CRAM input files" help="Data is in sorted cram files." />
+				</when>
+				<when value="pickle">
+					<param name="input_data" type="data" format="binary" multiple="true" label="PICKLE input files" help="Data is in one or more pickle file(s) from using NanoComp/NanoPlot." />
+				</when>
+				<when value="arrow">
+					<param name="input_data" type="data" format="binary" multiple="true" label="ARROW input files" help="Data is in one or more feather/arrow file(s)." />
+				</when>
+			</conditional>
+		</section>	
+
+		<section name="filters" title="Filtering Input Prior To Plotting" expanded="false">
+			<param argument="--maxlength" type="integer" optional="true" label="Max read length filtering" help="Drop reads longer than length specified." />
+			<param argument="--minlength" type="integer" optional="true" label="Min read length filtering" help="Drop reads shorter than length specified." />
+		</section>
+
+		<section name="plot_options" title="Plot Customization Options" expanded="false">
+			<param argument="--plot" type="select" label="Plot Type" help="Specify the type of plot to be used.">
+				<option value="box">Box plot</option>
+				<option value="violin" selected="true">Violin plot</option>
+				<option value="ridge">Ridge (joyplot) plot</option>
+				<option value="not">No plot</option>
+			</param>
+			<param argument="--title" type="text" label="Custom plot titles" help="Add a title to all plots." />
+			<param argument="--names" type="text" label="Custom names" help="Specify the names (space seperated, respective to input) to be used for the datasets." />
+			<param argument="--colors" type="text" label="Custom colors" help="Specify the colors (space seperated, respective to input) to be used for each the datasets. Can be any valid Matplotlib color: Named, HEX-string, RGB, ... " />
+		</section>	
+
+		<section name="output_options" title="Output Options" expanded="false">
+			<param argument="--tsv_stats" type="boolean" truevalue="--tsv_stats" falsevalue="" optional="true" checked="false" label="TSV Output Format" help="Output the statistics file as properly formatted TSV."/>
+		</section>
+
+	</inputs>
+
+
+	<outputs>
+		<data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log file"/>
+		<data name="stats_file" format="txt" from_work_dir="NanoStats.txt" label="${tool.name} on ${on_string}: Statistics file"/>	
+		<data name="html_report" format="html" from_work_dir="NanoComp-report.html" label="${tool.name} on ${on_string}: Html Report"/>	
+	</outputs>
+	<tests>
+		<test expect_num_outputs="3">
+			<section name="inputs">
+				<conditional name="input_type">	
+					<param name="input_type_selector" value="fastq" />
+					<param name="input_data" value="in1.fastq.gz,in2.fastq.gz,in3.fastq.gz" />
+				</conditional>
+			</section>
+			<output name="stats_file" > 
+				<assert_contents>
+					<has_text text="General summary" />
+				</assert_contents>
+			</output>
+			<output name="html_report"> 
+				<assert_contents>
+					<has_text text="html"/>
+					<has_text text="Summary statistics"/>
+				</assert_contents>
+			</output>
+		</test>
+		<test expect_num_outputs="3">
+			<section name="inputs">
+				<conditional name="input_type">
+					<param name="input_type_selector" value="bam" />
+					<param name="input_data" value="in4.bam,in5.bam" />
+				</conditional>
+			</section>
+			<section name="filters" >
+				<param name="maxlength" value="15000"/>
+				<param name="minlength" value="500"/>
+			</section>
+			<output name="html_report">
+				<assert_contents>
+					<has_text text="html"/>
+					<has_text text="Summary statistics"/>
+				</assert_contents>
+			</output>
+		</test>
+		<test expect_num_outputs="3">
+			<section name="inputs">
+				<conditional name="input_type">	
+					<param name="input_type_selector" value="fastq" />
+					<param name="input_data" value="in1.fastq.gz,in3.fastq.gz" />
+				</conditional>
+			</section>
+			<section name="output_options">
+				<param name="tsv_stats" value="true"/>
+			</section>
+			<output name="stats_file" > 
+			<assert_contents>
+				<has_text text="Metrics" />
+			</assert_contents>
+			</output>
+		</test>
+		<test expect_num_outputs="3">
+			<section name="inputs">
+				<conditional name="input_type">
+					<param name="input_type_selector" value="bam" />
+					<param name="input_data" value="in4.bam,in5.bam" />
+				</conditional>
+			</section>
+			<section name="plot_options" >
+		<param name="plot" value="box"/>
+			</section>
+			<output name="html_report">
+				<assert_contents>
+					<has_text text="html"/>
+					<has_text text="Plots"/>
+				</assert_contents>
+			</output>
+		</test>
+	</tests>
+	<help><![CDATA[
+**NanoComp** 
+
+Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot.
+
+**Usage Instructions**  
+
+Multiple input files (of the same type) are allowed
+
+**Output Files**  
+
+HTML file with the stats report and associated plots
+
+**More Information**  
+
+- **Official Repository**: [GitHub - wdecoster/nanocomp](https://github.com/wdecoster/nanocomp)  
+]]></help>
+	<citations>
+		<citation type="doi">10.1093/bioinformatics/btad311</citation>
+	</citations>
+</tool>
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