Mercurial > repos > bgruening > nanopolish_eventalign
diff nanopolish_eventalign.xml @ 0:bee42f615f28 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625
author | bgruening |
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date | Wed, 30 May 2018 11:55:18 -0400 |
parents | |
children | c8c5caecfacc |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nanopolish_eventalign.xml Wed May 30 11:55:18 2018 -0400 @@ -0,0 +1,128 @@ +<tool id="nanopolish_eventalign" name="Nanopolish eventalign" version="0.1.0"> + <description>- Align nanopore events to reference k-mers</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_merged' reads.fasta && + + #if $input_reads_raw.extension == 'fast5': + mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 && + #else + ln -s '$input_reads_raw' fast5_files.tar.gz && + mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files && + #end if + + nanopolish index -d fast5_files/ reads.fasta && + ln -s '$b' reads.bam && + ln -s '${b.metadata.bam_index}' reads.bam.bai && + ln -s '$g' genome.fa && + + nanopolish eventalign + -r reads.fasta + -b reads.bam + -g genome.fa + $samples + $scale_events + $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="h5,fast5.tar.gz" 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" /> + <param type="data" argument="-g" format="fasta" label="The reference genome"/> + + <!-- 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" /> + + <!-- 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 name="scale_events" argument="--scale-events" type="boolean" truevalue="--scale-events" falsevalue="" checked="false" + label="Scale events to the model, rather than vice-versa" /> + <param argument="--sam" type="boolean" truevalue="--sam" falsevalue="" checked="false" + label="write output in SAM format" /> + <param name="print_read_names" 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="Computed variants"/> + </outputs> + <tests> + <test> + <!-- index test --> + <param name="input_merged" ftype="fasta" value="reads.fasta" /> + <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> + + <!-- variants consensus test --> + <param name="b" value="reads.sorted.bam" /> + <param name="g" value="draft.fa" /> + <param name="w" value="tig00000001:200000-200010" /> + <param name="sam" value="true" /> + + <output name="output_summary" file="eventalign-summary.txt" /> + <output name="output_eventalign" file="reads-draft.eventalign.sam"/> + </test> + <test> + <!-- index test --> + <param name="input_merged" ftype="fasta" value="reads.fasta" /> + <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> + + <!-- variants consensus test --> + <param name="b" value="reads.sorted.bam" /> + <param name="g" 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" /> + + <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>