Mercurial > repos > iuc > nanocomp
changeset 3:8b2f1e817c9d draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp commit 69a2f2135f021f6e7bc35bce7b4954d2779efc07
| author | iuc |
|---|---|
| date | Fri, 12 Dec 2025 08:20:02 +0000 |
| parents | 0670dca750f7 |
| children | |
| files | nanocomp.xml |
| diffstat | 1 files changed, 170 insertions(+), 168 deletions(-) [+] |
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--- a/nanocomp.xml Tue Dec 02 17:29:44 2025 +0000 +++ b/nanocomp.xml Fri Dec 12 08:20:02 2025 +0000 @@ -1,26 +1,29 @@ <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@">1.25.6</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[ + <description>Compare multiple runs of long read sequencing data and alignments</description> + <macros> + <token name="@TOOL_VERSION@">1.25.6</token> + <token name="@VERSION_SUFFIX@">1</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 + + ##link input files with proper names (Nanocomp checks file-extensions) + #set $linked_files = [] #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 $in_name && + #if '.' in str($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' && + #silent $linked_files.append($in_name) #end for ##run nanocomp @@ -29,7 +32,7 @@ ##no need for the static images (becomes deprecated) --make_no_static - ## Compute options + ##Compute options --threads \${GALAXY_SLOTS:-4} ##add input files @@ -51,13 +54,9 @@ --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 + ## add the input files + #for $file in $linked_files + '$file' #end for ##Filter options @@ -94,148 +93,151 @@ >& $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> + <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="fastqsanger,fastqsanger.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="fastqsanger,fastqsanger.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="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="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> + <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> - + </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>< ]]></help> - <citations> - <citation type="doi">10.1093/bioinformatics/btad311</citation> - </citations> + <citations> + <citation type="doi">10.1093/bioinformatics/btad311</citation> + </citations> </tool>