comparison sortmerna.xml @ 3:59252ca85c74 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/sortmerna commit 5a8ffc52b7076d8d4fbc9649703bb4c0155b726c

2:3699b6b771e0

<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.0">
    <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
    <requirements>
        <requirement type="package" version="2.1b">sortmerna</requirement>
    </requirements>
    <stdio>

    	#end if
    	$aligned_sam.aligned_sam_selector
    	#if $aligned_sam.aligned_sam_selector == '--sam'
        	$aligned_sam.sq
    	#end if
    	$aligned_blast

    	$log

        #if $report.report_type == 'best'
            #if $report.report_best.report_best_type == '1'

            <when value="--sam">
                <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
            </when>
            <when value="" />
        </conditional>
        <param name="aligned_blast" type="select" label="Include alignments in BLAST-like format">
            <option value="--blast 0">pairwise (--blast 0)</option>
            <option value="--blast 1">tabular BLAST -m 8 format (--blast 1)</option>
            <option value="--blast 2">tabular + column for CIGAR (--blast 2)</option>
            <option value="--blast 3">tabular + columns for CIGAR and query coverage (--blast 3)</option>
            <option value="" selected="true">No</option>
        </param>
        <param name="log" type="boolean" checked="False" truevalue="--log" falsevalue="" label="Generate statistics file"
               help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
        </param>
	<conditional name="report">
            <param name="report_type" type="select" label="Parameters for filtering and read mapping" help="">
                <option value="best" selected="true">Report best alignments per read reaching E-value</option>

            label="Alignments on ${on_string} (SAM)">
            <filter>aligned_sam['aligned_sam_selector']</filter>
        </data>
        <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
            label="Alignments on ${on_string} (BLAST)">
            <filter>aligned_blast</filter>
            <change_format>
                <when input="aligned_blast" value="--blast 0" format="txt" />
            </change_format>
        </data>
        <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
            <filter>log</filter>
        </data>

            <param name="input_reads" value="read_small.fastq" />
            <param name="sequencing_type_selector" value="not_paired" />
            <param name="strand_search" value="" />
            <param name="databases_selector" value="history" />
            <param name="database_name" value="ref_small.fasta" />
            <param name="other" value="True" />
            <param name="log" value="" />
            <output name="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
            <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
            <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
        </test>
        <test>
            <param name="input_reads" value="read_small.fasta" />
            <param name="sequencing_type_selector" value="not_paired" />
            <param name="strand_search" value="" />
            <param name="databases_selector" value="history" />
            <param name="database_name" value="ref_small.fasta" />
            <param name="other" value="True" />
            <param name="log" value="" />
            <output name="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
            <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
            <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />
        </test>
    </tests>

3:59252ca85c74

<tool id="bg_sortmerna" name="Filter with SortMeRNA" version="2.1b.1">
    <description>Fast and accurate filtering of ribosomal RNAs in metatranscriptomic data</description>
    <requirements>
        <requirement type="package" version="2.1b">sortmerna</requirement>
    </requirements>
    <stdio>

    	#end if
    	$aligned_sam.aligned_sam_selector
    	#if $aligned_sam.aligned_sam_selector == '--sam'
        	$aligned_sam.sq
    	#end if
    	#if $aligned_blast.aligned_blast_selector == '--blast'
        	--blast "$aligned_blast.aligned_blast_format"
    	#end if

    	$log

        #if $report.report_type == 'best'
            #if $report.report_best.report_best_type == '1'

            <when value="--sam">
                <param name="sq" type="boolean" truevalue="--SQ" falsevalue="" label="Add SQ tags to the SAM file" help="(--SQ)" />
            </when>
            <when value="" />
        </conditional>
        <conditional name="aligned_blast">
            <param name="aligned_blast_selector" type="select" label="Include alignments in BLAST-like format?">
                <option value="--blast">Yes</option>
                <option value="" selected="true">No</option>
            </param>
            <when value="--blast">
                <param name="aligned_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="" />
        </conditional>
        <param name="log" type="boolean" checked="false" truevalue="--log" falsevalue="" label="Generate statistics file"
               help="Generates statistics for the rRNA content of reads, as well as rRNA subunit distribution. (--log)">
        </param>
	<conditional name="report">
            <param name="report_type" type="select" label="Parameters for filtering and read mapping" help="">
                <option value="best" selected="true">Report best alignments per read reaching E-value</option>

            label="Alignments on ${on_string} (SAM)">
            <filter>aligned_sam['aligned_sam_selector']</filter>
        </data>
        <data format="tabular" name="output_blast" from_work_dir="aligned.blast"
            label="Alignments on ${on_string} (BLAST)">
            <filter>aligned_blast['aligned_blast_selector']</filter>
            <change_format>
                <when input="aligned_blast.aligned_blast_format" value="0" format="txt" />
            </change_format>
        </data>
        <data format="txt" name="output_log" label="${tool.name} statistics (txt)" from_work_dir="aligned.log">
            <filter>log</filter>
        </data>

            <param name="input_reads" value="read_small.fastq" />
            <param name="sequencing_type_selector" value="not_paired" />
            <param name="strand_search" value="" />
            <param name="databases_selector" value="history" />
            <param name="database_name" value="ref_small.fasta" />
            <param name="aligned_fastx_selector" value="--fastx" />
            <param name="other" value="True" />
            <param name="aligned_sam_selector" value="--sam" />
            <param name="aligned_blast_selector" value="--blast"/>
            <param name="aligned_blast_format" value="1 cigar qcov" />
            <param name="log" value="" />
            <param name="report_type" value="best" />
            <param name="report_best_type" value="1" />
            <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="output_fastx" file="sortmerna_wrapper_accept1.fastq" />
            <output name="output_other" file="sortmerna_wrapper_other1.fastq" />
            <output name="output_sam" file="sortmerna_wrapper_sam1.sam" lines_diff="2" />
        </test>
        <test>
            <param name="input_reads" value="read_small.fasta" />
            <param name="sequencing_type_selector" value="not_paired" />
            <param name="strand_search" value="" />
            <param name="databases_selector" value="history" />
            <param name="database_name" value="ref_small.fasta" />
            <param name="aligned_fastx_selector" value="--fastx" />
            <param name="other" value="True" />
            <param name="aligned_sam_selector" value="--sam" />
            <param name="aligned_blast" value="" />
            <param name="log" value="" />
            <param name="report_type" value="best" />
            <param name="report_best_type" value="1" />
            <param name="report_type" value="best" />
            <param name="report_best_type" value="1" />
            <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="output_fastx" file="sortmerna_wrapper_accept2.fasta" />
            <output name="output_other" file="sortmerna_wrapper_other2.fasta" />
            <output name="output_sam" file="sortmerna_wrapper_sam2.sam" lines_diff="2" />
        </test>
    </tests>