comparison sortmerna.xml @ 9:eb35257d2e29 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit d83142dbe2432fcb0f56dcd6311a05c061628ecc

8:65c38d020fea

<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.5">
    <description>of ribosomal RNAs in metatranscriptomic data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">sortmerna</requirement>
        <requirement type="package" version="1.5">samtools</requirement>
    </requirements>

        #end for
    #end if

    #if str( $databases_type.databases_selector ) != 'cached'
        indexdb_rna 
            --ref $ref 
            -L $databases_type.seed_length 
            --max_pos $databases_type.max_pos 
        &&
    #end if

    #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
        merge-paired-reads.sh
            '$sequencing_type.forward_reads'
            '$sequencing_type.reverse_reads'
            merged-reads.fastq
        &&
    #end if

    sortmerna 
        --ref $ref
        --aligned aligned
        #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
            --reads merged-reads.fastq
            $sequencing_type.paired_type
        #else
            --reads '$sequencing_type.reads'
        #end if
        $strand_search
        $log
        $aligned_fastx.aligned_fastx_selector
        #if $aligned_fastx.aligned_fastx_selector == '--fastx'
            #if $aligned_fastx.other
                --other unaligned
            #end if
        #end if
        #if $report.report_type == 'best'
            @ALIGNMENTS@
            #if $report.otu.otu_map == 'True'

        -e '$e_value'
        --match '$match'
        --mismatch '$mismatch'
        --gap_open '$gap_open'
        --gap_ext '$gap_ext'
        -N $ambiguous_letter
        -a \${GALAXY_SLOTS:-1}
    #if $report.report_type != 'None'
        &&
        samtools view -@ "\${GALAXY_SLOTS:-4}" -u aligned.sam | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o '$output_bam'
    #end if

    #if str( $sequencing_type.sequencing_type_selector ) == 'paired' and $sequencing_type.paired_type != '' and $aligned_fastx.aligned_fastx_selector == '--fastx'
        &&
        unmerge-paired-reads.sh
            aligned.fastq
            '$aligned_forward'
            '$aligned_reverse'
        #if $aligned_fastx.other
            &&
            unmerge-paired-reads.sh
                unaligned.fastq
                '$unaligned_forward'
                '$unaligned_reverse'
        #end if
    #end if
]]>
    </command>
    <inputs>

            </param>
            <when value="not_paired">
                <param argument="--reads" type="data" format="fasta,fastq" label="Querying sequences"/>
            </when>
            <when value="paired">
                <param name="forward_reads" type="data" format="fastq" label="Forward reads"/>
                <param name="reverse_reads" type="data" format="fastq" label="Reverse reads"/>
                <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
                    <option value="">Leave the reads split between aligned and rejected files</option>
                    <option value="--paired_in">Output both reads to aligned file (--paired_in)</option>
                    <option value="--paired_out">Output both reads to rejected file (--paired_out)</option>
                </param>

    </inputs>
    <outputs>
        <data name="output_fastx" format_source="reads" from_work_dir="aligned.dat" label="${tool.name} on ${on_string}: Aligned reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] != 'paired'</filter>
        </data>
        <data name="output_paired_fastx" format="fastq" from_work_dir="aligned.fastq" label="${tool.name} on ${on_string}: Aligned reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] == ''</filter>
        </data>
        <data name="aligned_forward" format="fastq" label="${tool.name} on ${on_string}: Aligned forward reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != ''  and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
        </data>
        <data name="aligned_reverse" format="fastq" label="${tool.name} on ${on_string}: Aligned reverse reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != ''  and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
        </data>
        <data name="output_other" format_source="reads" from_work_dir="unaligned.dat" label="${tool.name} on ${on_string}: Unaligned reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'not_paired'</filter>
        </data>
        <data name="output_paired_other" format="fastq" from_work_dir="unaligned.fastq" label="${tool.name} on ${on_string}: Unaligned reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] == ''</filter>
        </data>
        <data name="unaligned_forward" format="fastq" label="${tool.name} on ${on_string}: Unaligned forward reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
        </data>
        <data name="unaligned_reverse" format="fastq" label="${tool.name} on ${on_string}: Unaligned reverse reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
        </data>
        <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: Alignments">
            <filter>report['report_type'] != 'None'</filter>
        </data>

            <param name="ambiguous_letter" value="-3"/>
            <output name="output_bam" file="test4_bam.bam" compare="sim_size" delta="200" />
            <output name="output_biom" file="test4_biom.txt"/>
            <output name="output_de_novo" file="test4_de_novo.fasta"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

9:eb35257d2e29

<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="@VERSION@.6">
    <description>of ribosomal RNAs in metatranscriptomic data</description>
    <macros>
        <token name="@VERSION@">2.1b</token>
        <xml name="db_prep">
            <param name="seed_length" type="integer" min="0" max="100" value="18" label="Seed length for database indexing" help="(-L)"/>
            <param name="max_pos" type="integer" min="0" max="100000" value="10000" label="Maximum number of positions to store for each k-mer for database indexing" help="With 0, all positions are stored (--max_pos)"/>
        </xml>
        <xml name="output_alignments">
            <param name="print_all_reads" type="boolean" checked="false" truevalue="--print_all_reads" falsevalue="" label="Output null alignment strings for non-aligned reads"/>
            <conditional name="blast">
                <param name="blast_output" type="select" label="Output BLAST report?">
                    <option value="True">Yes</option>
                    <option value="False" selected="True">No</option>
                </param>
                <when value="True">
                    <param name="blast_format" type="select" label="BLAST-like format?">
                        <option value="0">pairwise (--blast '0')</option>
                        <option value="1">tabular BLAST -m 8 format (--blast '1')</option>
                        <option value="1 cigar">tabular + column for CIGAR (--blast '1 cigar')</option>
                        <option value="1 cigar qcov">tabular + columns for CIGAR and query coverage (--blast '1 cigar qcov')</option>
                        <option value="1 cigar qcov qstrand">tabular + columns for CIGAR, query coverage and strand (--blast '1 cigar qcov qstrand')</option>
                    </param>
                </when>
                <when value="False"/>
            </conditional>
        </xml>
        <token name="@ALIGNMENTS@">
            $report.print_all_reads
            --sam
            --SQ
            #if $report.blast.blast_output == 'True'
                --blast '$report.blast.blast_format'
            #end if
        </token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">sortmerna</requirement>
        <requirement type="package" version="1.5">samtools</requirement>
    </requirements>

        #end for
    #end if

    #if str( $databases_type.databases_selector ) != 'cached'
        indexdb_rna 
            --ref '$ref'
            -L '$databases_type.seed_length'
            --max_pos '$databases_type.max_pos'
        &&
    #end if

    #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
        merge-paired-reads.sh
            '$sequencing_type.forward_reads'
            '$sequencing_type.reverse_reads'
            merged-reads
        &&
    #end if

    sortmerna 
        --ref '$ref'
        --aligned 'aligned'
        #if str( $sequencing_type.sequencing_type_selector ) == 'paired'
            --reads 'merged-reads'
            $sequencing_type.paired_type
        #else
            --reads '$sequencing_type.reads'
        #end if
        $strand_search
        $log
        $aligned_fastx.aligned_fastx_selector
        #if $aligned_fastx.aligned_fastx_selector == '--fastx'
            #if $aligned_fastx.other
                --other 'unaligned'
            #end if
        #end if
        #if $report.report_type == 'best'
            @ALIGNMENTS@
            #if $report.otu.otu_map == 'True'

        -e '$e_value'
        --match '$match'
        --mismatch '$mismatch'
        --gap_open '$gap_open'
        --gap_ext '$gap_ext'
        -N '$ambiguous_letter'
        -a \${GALAXY_SLOTS:-1}
    #if $report.report_type != 'None'
        &&
        samtools view -@ "\${GALAXY_SLOTS:-4}" -u aligned.sam | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o '$output_bam'
    #end if

    #if $aligned_fastx.aligned_fastx_selector == '--fastx' and str($sequencing_type.sequencing_type_selector) == 'paired'
        #if str($sequencing_type.paired_type) != ''
            &&
            unmerge-paired-reads.sh
                aligned.fast*
                '$aligned_forward'
                '$aligned_reverse'
            #if $aligned_fastx.other
                &&
                unmerge-paired-reads.sh
                    unaligned.fast*
                    '$unaligned_forward'
                    '$unaligned_reverse'
            #end if
        #else
            &&
            mv aligned.fast* '$aligned_paired'
            #if $aligned_fastx.other
                &&
                mv unaligned.fast* '$unaligned_paired'
            #end if
        #end if
    #end if
]]>
    </command>
    <inputs>

            </param>
            <when value="not_paired">
                <param argument="--reads" type="data" format="fasta,fastq" label="Querying sequences"/>
            </when>
            <when value="paired">
                <param name="forward_reads" type="data" format="fasta,fastq" label="Forward reads"/>
                <param name="reverse_reads" type="data" format="fasta,fastq" label="Reverse reads"/>
                <param name="paired_type" type="select" display="radio" label="If one of the paired-end reads aligns and the other one does not">
                    <option value="">Leave the reads split between aligned and rejected files</option>
                    <option value="--paired_in">Output both reads to aligned file (--paired_in)</option>
                    <option value="--paired_out">Output both reads to rejected file (--paired_out)</option>
                </param>

    </inputs>
    <outputs>
        <data name="output_fastx" format_source="reads" from_work_dir="aligned.dat" label="${tool.name} on ${on_string}: Aligned reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] != 'paired'</filter>
        </data>
        <data name="aligned_paired" format_source="forward_reads" label="${tool.name} on ${on_string}: Aligned reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] == ''</filter>
        </data>
        <data name="aligned_forward" format_source="forward_reads" label="${tool.name} on ${on_string}: Aligned forward reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
        </data>
        <data name="aligned_reverse" format_source="reverse_reads" label="${tool.name} on ${on_string}: Aligned reverse reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
        </data>
        <data name="output_other" format_source="reads" from_work_dir="unaligned.dat" label="${tool.name} on ${on_string}: Unaligned reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] != 'paired'</filter>
        </data>
        <data name="unaligned_paired" format_source="forward_reads" label="${tool.name} on ${on_string}: Unaligned reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] == ''</filter>
        </data>
        <data name="unaligned_forward" format_source="forward_reads" label="${tool.name} on ${on_string}: Unaligned forward reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
        </data>
        <data name="unaligned_reverse" format_source="reverse_reads" label="${tool.name} on ${on_string}: Unaligned reverse reads">
            <filter>aligned_fastx['aligned_fastx_selector'] != '' and aligned_fastx['other'] == True and sequencing_type['sequencing_type_selector'] == 'paired' and sequencing_type['paired_type'] != ''</filter>
        </data>
        <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: Alignments">
            <filter>report['report_type'] != 'None'</filter>
        </data>

            <param name="ambiguous_letter" value="-3"/>
            <output name="output_bam" file="test4_bam.bam" compare="sim_size" delta="200" />
            <output name="output_biom" file="test4_biom.txt"/>
            <output name="output_de_novo" file="test4_de_novo.fasta"/>
        </test>
        <test>
            <conditional name="sequencing_type">
                <param name="sequencing_type_selector" value="paired" />
                <param name="forward_reads" value="forward_reads.fasta" />
                <param name="reverse_reads" value="reverse_reads.fasta" />
                <param name="paired_type" value=""/>
            </conditional>
            <param name="strand_search" value="" />
            <conditional name="databases_type">
                <param name="databases_selector" value="history" />
                <param name="database_name" value="ref_small.fasta" />
                <param name="seed_length" value="18" />
                <param name="max_pos" value="100000"/>
            </conditional>
            <conditional name="aligned_fastx">
                <param name="aligned_fastx_selector" value="--fastx" />
                <param name="other" value="True" />
            </conditional>
            <param name="log" value="False" />
            <conditional name="report">
                <param name="report_type" value="best" />
                <param name="report_num_alignments_type" value="1"/>
                <param name="print_all_reads" value="False" />
                <conditional name="blast">
                    <param name="blast_output" value="False"/>
                </conditional>
                <conditional name="otu">
                    <param name="otu_map" value="False"/>
                </conditional>
            </conditional>
            <param name="e_value" value="1"/>
            <param name="match" value="2"/>
            <param name="mismatch" value="-3" />
            <param name="gap_open" value="5"/>
            <param name="gap_ext" value="2"/>
            <param name="ambiguous_letter" value="-3"/>
            <output name="aligned_paired" file="test5_aligned.fasta" />
            <output name="unaligned_paired" file="test5_unaligned.fasta" />
        </test>
        <test>
            <conditional name="sequencing_type">
                <param name="sequencing_type_selector" value="paired" />
                <param name="forward_reads" value="forward_reads.fasta" />
                <param name="reverse_reads" value="reverse_reads.fasta" />
                <param name="paired_type" value="--paired_out"/>
            </conditional>
            <param name="strand_search" value="" />
            <conditional name="databases_type">
                <param name="databases_selector" value="history" />
                <param name="database_name" value="ref_small.fasta" />
                <param name="seed_length" value="18" />
                <param name="max_pos" value="100000"/>
            </conditional>
            <conditional name="aligned_fastx">
                <param name="aligned_fastx_selector" value="--fastx" />
                <param name="other" value="True" />
            </conditional>
            <param name="log" value="False" />
            <conditional name="report">
                <param name="report_type" value="best" />
                <param name="report_num_alignments_type" value="1"/>
                <param name="print_all_reads" value="False" />
                <conditional name="blast">
                    <param name="blast_output" value="False"/>
                </conditional>
                <conditional name="otu">
                    <param name="otu_map" value="False"/>
                </conditional>
            </conditional>
            <param name="e_value" value="1"/>
            <param name="match" value="2"/>
            <param name="mismatch" value="-3" />
            <param name="gap_open" value="5"/>
            <param name="gap_ext" value="2"/>
            <param name="ambiguous_letter" value="-3"/>
            <output name="aligned_forward" file="test6_aligned_forward.fasta" />
            <output name="aligned_reverse" file="test6_aligned_reverse.fasta" />
            <output name="unaligned_forward" file="test6_unaligned_forward.fasta" />
            <output name="unaligned_reverse" file="test6_unaligned_reverse.fasta" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**