Mercurial > repos > bgruening > nanopolish_eventalign
view nanopolish_eventalign.xml @ 8:3b6f94fc7e1d draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4
author | bgruening |
---|---|
date | Thu, 30 Nov 2023 17:58:54 +0000 |
parents | 855b7ba0ce9c |
children |
line wrap: on
line source
<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> <description>- Align nanopore events to reference k-mers</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @PREPROCESS_INPUTS@ nanopolish eventalign -r reads.fasta -b reads.bam -g genome.fa #if str($min_mapping_quality): -q $min_mapping_quality #end if --threads "\${GALAXY_SLOTS:-4}" $samples $scale_events $signal_index $sam $print_read_names #if $w and str($w).strip(): -w "${w}" #end if #if $input_models_fofn: --models-fofn '$input_models_fofn' #end if #if $summary: --summary eventalign-summary.txt #end if > eventalign.out ]]></command> <inputs> <!-- index inputs --> <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> <param type="data" name="input_reads_raw" format="fast5.tar.xz,fast5.tar.gz,fast5.tar.bz2,fast5.tar,fast5" label="Flat archive file of raw fast5 files"/> <!-- variants consensus inputs --> <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> <conditional name="reference_source"> <param name="reference_source_selector" type="select" label="Load reference genome from"> <option value="cached">Local cache</option> <option value="history">History</option> </param> <when value="cached"> <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> <options from_data_table="all_fasta"> </options> <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> </param> </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> </when> </conditional> <section name="adv" title="Optional data inputs"> <!-- optional inputs --> <param type="data" name="input_seq_summary" format="txt" optional="true" label="Sequencing summary file from albacore" help="(-s)"/> </section> <!-- optional inputs --> <param type="data" name="input_models_fofn" argument="--models-fofn" format="txt" optional="true" label="Read alternative k-mer models (optional)" /> <!-- optional params --> <param argument="-w" type="text" optional="true" label="find variants in window of region chromsome:start-end" /> <param name="min_mapping_quality" type="integer" optional="true" value="" label="Only use reads with mapping quality of at least this value" help="(-q)"/> <!-- optional flags --> <param argument="--summary" type="boolean" truevalue="--summary" falsevalue="" checked="true" label="Summarize the alignment of each read/strand" /> <param argument="--samples" type="boolean" truevalue="--samples" falsevalue="" checked="false" label="Write the raw samples for the event to the tsv output" /> <param argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" label="Scale events to the model, rather than vice-versa" /> <param argument="--signal-index" type="boolean" truevalue="--signal-index" falsevalue="" checked="false" label="write the raw signal start and end index values for the event to the tsv output" /> <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false" label="write output in SAM format" /> <param argument="--print-read-names" type="boolean" truevalue="--print-read-names" falsevalue="" checked="false" label="Print read names instead of indexes" /> </inputs> <outputs> <!-- variants consensus outputs --> <data name="output_summary" format="txt" from_work_dir="eventalign-summary.txt" label="eventalign summary of reads/strands" /> <data name="output_eventalign" format="txt" from_work_dir="eventalign.out" label="Aligned squiggles"/> </outputs> <tests> <test> <param name="input_merged" ftype="fasta" value="reads.fasta" /> <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> <param name="b" value="reads.sorted.bam" /> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="draft.fa" /> <param name="w" value="tig00000001:200000-200010" /> <param name="sam" value="true" /> <output name="output_summary" file="eventalign-summary.txt" compare="sim_size"> <assert_contents> <has_n_lines n="144"/> <has_n_columns n="14"/> <has_line_matching expression="read_index\sread_name\sfast5_path\smodel_name\sstrand\snum_events\snum_steps\snum_skips\snum_stays\stotal_duration\sshift\sscale\sdrift\svar"/> <has_text text="d57afb7d-903e-46cf-a43d-0e17fb0949d8"/> <has_text text="15727"/> <has_text text="fast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read5665_strand.fast5"/> </assert_contents> </output> <output name="output_eventalign" file="reads-draft.eventalign.sam" compare="sim_size"> <assert_contents> <has_n_lines n="148"/> <has_line_matching expression="@SQ\sSN:tig00000001\sLN:4376233"/> <has_text text="d57afb7d-903e-46cf-a43d-0e17fb0949d8"/> <has_text text="191118"/> <has_text text="274S1M2I3M1I2M2I9M1I1M1I1M1I9M6I3M1I1M2I2M2I2M1"/> </assert_contents> </output> </test> <test> <param name="input_merged" ftype="fasta" value="reads.fasta" /> <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> <param name="b" value="reads.sorted.bam" /> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="draft.fa" /> <param name="w" value="tig00000001:200000-200010" /> <param name="sam" value="false" /> <param name="summary" value="false" /> <param name="scale_events" value="true" /> <param name="print_read_names" value="true" /> <param name="min_mapping_quality" value="0" /> <output name="output_summary" file="t2-eventalign-summary.txt" /> <output name="output_eventalign"> <assert_contents> <has_text text="contig" /> <has_text text="position" /> <has_text text="event_index" /> <has_text text="tig00000001" /> </assert_contents> </output> </test> <test> <!-- test data table reference --> <param name="input_merged" ftype="fasta" value="reads.fasta" /> <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> <param name="b" value="reads.sorted.bam" /> <param name="reference_source_selector" value="history" /> <param name="ref_file" value="draft.fa"/> <param name="w" value="tig00000001:200000-200010" /> <param name="sam" value="false" /> <param name="summary" value="false" /> <param name="scale_events" value="true" /> <param name="print_read_names" value="true" /> <param name="min_mapping_quality" value="0" /> <output name="output_summary" file="t2-eventalign-summary.txt" /> <output name="output_eventalign"> <assert_contents> <has_text text="contig" /> <has_text text="position" /> <has_text text="event_index" /> <has_text text="tig00000001" /> </assert_contents> </output> </test> </tests> <help><![CDATA[ Usage: nanopolish eventalign [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa Align nanopore events to reference k-mers Tutorial and manual available at: http://nanopolish.readthedocs.io/en/latest/quickstart_eventalign.html ]]></help> <expand macro="citations" /> </tool>