comparison nanopolish_variants.xml @ 8:bec636361cfd draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit de2370d1a385731b3c65f1dcc44e7b8558da8fd4

7:a3afc5f0a96c

<tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy0">
    <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</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 if $input_reads_raw.extension == 'fast5.tar':
            ln -s '$input_reads_raw' fast5_files.tar &&
            mkdir fast5_files && tar -xf fast5_files.tar -C fast5_files &&

        #else if $input_reads_raw.extension == 'fast5.tar.bz2':
            ln -s '$input_reads_raw' fast5_files.tar.bz2 &&
            mkdir fast5_files && tar -xjf fast5_files.tar.bz2 -C fast5_files &&

        #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/
        #if $adv.input_seq_summary:
          -s '$adv.input_seq_summary'
        #end if 
        reads.fasta &&
        
        ln -s '$b' reads.bam &&
        ln -s '${b.metadata.bam_index}' reads.bam.bai &&
        #if $reference_source.reference_source_selector == 'history':
            ln -f -s '$reference_source.ref_file' genome.fa &&
        #else:
            ln -f -s '$reference_source.ref_file.fields.path' genome.fa &&
        #end if
        
        nanopolish variants
        -r reads.fasta
        -b reads.bam
        -g genome.fa

        #end if
        #if $adv.input_models_fofn:
          --models-fofn '$input_models_fofn'
        #end if

        && 

        nanopolish vcf2fasta --skip-checks -g genome.fa variants.vcf > polished.fa


    ]]></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.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>

            <param type="data" name="input_alt_bc_bam" format="bam" optional="true" label="Alternative basecaller used that does not output event annotations" help="(-a)" />
            <param type="data" name="input_models_fofn" format="txt" optional="true" label="Read alternative k-mer models" help="(--models-fofn)" />
       </section>

        <!-- optional params -->
        <!-- optional params -->
        <param argument="-w" type="text" optional="true"
            label="find variants in window of region chromsome:start-end" />
        <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/>
        <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/>
        <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/>

        </test>
    </tests>
    <help><![CDATA[

        Build an index mapping from basecalled reads to the signals measured by the sequencer
        and
        Find SNPs using a signal-level HMM

        Tutorial and manual available at:
        http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html

8:bec636361cfd

<tool id="nanopolish_variants" name="Nanopolish variants" version="@VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>- Find SNPs of basecalled merged Nanopore reads and polishes the consensus sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
        @PREPROCESS_INPUTS@
        
        nanopolish variants
        -r reads.fasta
        -b reads.bam
        -g genome.fa

        #end if
        #if $adv.input_models_fofn:
          --models-fofn '$input_models_fofn'
        #end if

        &&
        nanopolish vcf2fasta
            --skip-checks
            -g genome.fa
            variants.vcf > polished.fa
    ]]></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.gz,fast5.tar.bz2,fast5.tar" label="Flat archive file of raw fast5 files"/>

            <param type="data" name="input_alt_bc_bam" format="bam" optional="true" label="Alternative basecaller used that does not output event annotations" help="(-a)" />
            <param type="data" name="input_models_fofn" format="txt" optional="true" label="Read alternative k-mer models" help="(--models-fofn)" />
       </section>

        <!-- optional params -->
        <param argument="-w" type="text" optional="true"
            label="find variants in window of region chromsome:start-end" />
        <param name="methylation_aware" type="text" optional="true" label="methylation aware polishing and test motifs given" help="(-q)"/>
        <param name="min_candidate_frequency" type="float" optional="true" value="0.2" label="Extarct if the variant frequency is at least F" help="(-m)"/>
        <param name="min_candidate_depth" type="integer" optional="true" value="20" label="Extarct if the depth is at least D" help="(-d)"/>

        </test>
    </tests>
    <help><![CDATA[

        Build an index mapping from basecalled reads to the signals measured by the sequencer
        and find SNPs using a signal-level HMM.

        Tutorial and manual available at:
        http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html