comparison bbmerge.xml @ 2:16db2a5b73c5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit cd59ba2c349865259b92302a1d70e103b8a5e3cb

1:03646ca53c91

    <description>Merge overlapping mates of a read pair</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#import os
#import re

#if str($input_type_cond.input_type) in ['single', 'pair']:
    #set read1 = $input_type_cond.read1
    ## bbmerge uses the file extension to determine the input format.
    #set ext = '.fastq'
    #if $read1.ext.endswith('.gz'):

        #set read2_file = 'reverse' + $ext
        ln -s '${read2}' '${read2_file}' &&
    #end if
#else:
    #set read1 = $input_type_cond.reads_collection['forward']
    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
    ## bbmap uses the file extension to determine the input format.
    #set ext = $read1_identifier + '.fastq'
    #if $read1.ext.endswith('.gz'):
        #set ext = $ext + '.gz'
    #end if
    #set read1_file = $read1_identifier + $ext
    ln -s '${read1}' '${read1_file}' &&
    #set read2 = $input_type_cond.reads_collection['reverse']
    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
    #set read2_file = $read2_identifier + $ext
    ln -s '${read2}' '${read2_file}' &&
#end if

bbmerge.sh
#### Input parameters
#if str($input_type_cond.input_type) == 'single':
    in='${read1_file}'
    interleaved=t
#else:

$merge_options.strictness=t
]]></command>
    <inputs>
        <expand macro="input_type_cond"/>
        
        <section name="qt_options" title="Quality and trimming options">
            <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
                <option value="f" selected="true">No trimming</option>
                <option value="l">Trim left</option>
                <option value="r">Trim right</option>

            </param>
            <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
            <param argument="minlength_after_trim" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
            <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
        </section>
        
        <section name="merge_options" title="Merging parameters">
            <param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
                <option value="xstrict">max strict</option>
                <option value="ustrict">ultra strict</option>
                <option value="vstrict">very strict</option>

            </param>
            <param argument="ecco" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Error-correct the overlapping part, but don't merge." help="If selected, the tool with find the overlaps as if merging reads, use this overlap information to correct sequencing errors on both strands. However, the strands from the mates will not be merged but provided as two separate reads after error correction."/>
            <param argument="trimnonoverlapping" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim all non-overlapping portions, leaving only consensus sequence. By default, only sequence to the right of the overlap (adapter sequence) is trimmed."/>
            <param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
            <param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>
            
            <param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
            <param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>
            
            <param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
            <param argument="efilter" type="integer" value="6" label="Ban overlaps with over this many times the expected number of errors." help="Lower is more strict, -1 disables."/>
            <param argument="pfilter" type="float" value="0.00004" label="Probability filter to disallow improbable overlaps." help="Higher is stricter. 0 will disable the filter; 1 will allow only perfect overlaps."/>
            <param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
            <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Take quality factors into account" help="If disabled, quality values are completely ignored, both for overlap detection and filtering. May be useful for data with inaccurate quality values."/>
            
            <conditional name="adapters">
                <param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
                    <option value="wout_adapters" selected="true">No</option>
                    <option value="with_adapters">Yes, use these adapter sequences</option>
                </param>

                <when value="with_adapters">
                    <param argument="adapter1" type="text" value="" label="Left adapter sequence"/>
                    <param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
                </when>
            </conditional>

            <conditional name="merge_mode">
                <param name="selector" type="select" label="Evaluate overlaps via..." help="In the ratio mode, overlaps are decided based on the ratio of matching to mismatching bases. Flat mode scores overlaps based on the total number of mismatching bases only.">
                    <option value="Ratio mode" selected="true">Ratio mode</option>
                    <option value="Flat mode">Flat mode</option>
                </param>

    +
    FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF
    </help>
    <expand macro="citations"/>
</tool>

2:16db2a5b73c5

    <description>Merge overlapping mates of a read pair</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="bio.tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
#if str($input_type_cond.input_type) in ['single', 'pair']:
    #set read1 = $input_type_cond.read1
    ## bbmerge uses the file extension to determine the input format.
    #set ext = '.fastq'
    #if $read1.ext.endswith('.gz'):

        #set read2_file = 'reverse' + $ext
        ln -s '${read2}' '${read2_file}' &&
    #end if
#else:
    #set read1 = $input_type_cond.reads_collection['forward']
    ## bbmap uses the file extension to determine the input format.
    #set ext = '.fastq'
    #if $read1.ext.endswith('.gz'):
        #set ext = $ext + '.gz'
    #end if
    #set read1_file = 'forward' + $ext
    ln -s '${read1}' '${read1_file}' &&
    #set read2 = $input_type_cond.reads_collection['reverse']
    #set read2_file = 'reverse' + $ext
    ln -s '${read2}' '${read2_file}' &&
#end if

if [[ "\${_JAVA_OPTIONS}" != *-Xmx* && "\${JAVA_TOOL_OPTIONS}" != *-Xmx* ]]; then
    export _JAVA_OPTIONS="\${_JAVA_OPTIONS} -Xmx\${GALAXY_MEMORY_MB:-4096}m -Xms256m";
fi &&

bbmerge.sh tmpdir="\$TMPDIR" t="\${GALAXY_SLOTS:-2}"

#### Input parameters
#if str($input_type_cond.input_type) == 'single':
    in='${read1_file}'
    interleaved=t
#else:

$merge_options.strictness=t
]]></command>
    <inputs>
        <expand macro="input_type_cond"/>
        <section name="qt_options" title="Quality and trimming options">
            <param name="qtrim" type="select" label="Select option for quality trimming ends before mapping">
                <option value="f" selected="true">No trimming</option>
                <option value="l">Trim left</option>
                <option value="r">Trim right</option>

            </param>
            <param argument="trimq" type="integer" value="6" label="Trim regions with average quality below this value"/>
            <param argument="minlength_after_trim" type="integer" value="60" label="Don't trim reads to be shorter than this value"/>
            <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Use quality scores when determining which read kmers to use as seeds?"/>
        </section>
        <section name="merge_options" title="Merging parameters">
            <param name="strictness" type="select" label="Select option for quality trimming ends before mapping">
                <option value="xstrict">max strict</option>
                <option value="ustrict">ultra strict</option>
                <option value="vstrict">very strict</option>

            </param>
            <param argument="ecco" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Error-correct the overlapping part, but don't merge." help="If selected, the tool with find the overlaps as if merging reads, use this overlap information to correct sequencing errors on both strands. However, the strands from the mates will not be merged but provided as two separate reads after error correction."/>
            <param argument="trimnonoverlapping" type="boolean" truevalue="t" falsevalue="f" checked="false" label="Trim all non-overlapping portions, leaving only consensus sequence. By default, only sequence to the right of the overlap (adapter sequence) is trimmed."/>
            <param argument="mininsert" type="integer" value="35" label="Minimum insert size to merge reads"/>
            <param argument="minoverlap" type="integer" value="12" label="Minimum number of overlapping bases to allow merging"/>
            <param argument="minq" type="integer" value="9" label="Ignore bases with quality below this"/>
            <param argument="maxq" type="integer" value="41" label="Cap output quality scores at this"/>
            <param argument="entropy" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Increase the minimum overlap requirement for low-complexity reads"/>
            <param argument="efilter" type="integer" value="6" label="Ban overlaps with over this many times the expected number of errors." help="Lower is more strict, -1 disables."/>
            <param argument="pfilter" type="float" value="0.00004" label="Probability filter to disallow improbable overlaps." help="Higher is stricter. 0 will disable the filter; 1 will allow only perfect overlaps."/>
            <param argument="kfilter" type="integer" value="41" label="Ban overlaps that create kmers with count below this value" help="Requires good coverage, 0 disables."/>
            <param argument="usequality" type="boolean" truevalue="t" falsevalue="f" checked="true" label="Take quality factors into account" help="If disabled, quality values are completely ignored, both for overlap detection and filtering. May be useful for data with inaccurate quality values."/>
            <conditional name="adapters">
                <param name="selector" type="select" label="Provide adapter sequences to improve accuracy?">
                    <option value="wout_adapters" selected="true">No</option>
                    <option value="with_adapters">Yes, use these adapter sequences</option>
                </param>

                <when value="with_adapters">
                    <param argument="adapter1" type="text" value="" label="Left adapter sequence"/>
                    <param argument="adapter2" type="text" value="" label="Right adapter sequence"/>
                </when>
            </conditional>
            <conditional name="merge_mode">
                <param name="selector" type="select" label="Evaluate overlaps via..." help="In the ratio mode, overlaps are decided based on the ratio of matching to mismatching bases. Flat mode scores overlaps based on the total number of mismatching bases only.">
                    <option value="Ratio mode" selected="true">Ratio mode</option>
                    <option value="Flat mode">Flat mode</option>
                </param>

    +
    FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF
    </help>
    <expand macro="citations"/>
</tool>