comparison flash.xml @ 2:b48895989d78 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit e365f2835488e73b870c73502c24ff23d28b76a5

1:d043b54b3bfb

<?xml version="1.0"?>
<tool id="flash" name="FLASH" version="@VERSION@.1">
    <description>adjust length of short reads</description>
    <requirements>
        <requirement type="package" version="@VERSION@">flash</requirement>
    </requirements>
    <macros>
        <token name="@VERSION@">1.2.11</token>
    </macros>
    <version_command>flash --version | head -n 1</version_command>
    <command detect_errors="aggressive">
        <![CDATA[
            flash --threads=\${GALAXY_SLOTS:-1}
                -m $min_overlap
                -M $max_overlap
                -x $max_mismatch_density
                $allow_outies
                #if $layout.select_layout == 'individual':
                    '$layout.forward' '$layout.reverse'
                #else:
                    '$layout.reads.forward' '$layout.reads.reverse'
                #end if
        ]]>
    </command>
    <inputs>
        <conditional name="layout">
            <param name="select_layout" type="select">
                <option value="individual">Individual datasets</option>
                <option value="collection">Paired collection</option>
            </param>
            <when value="individual">
                <param format="fastq" name="forward" type="data" label="Forward reads" />
                <param format="fastq" name="reverse" type="data" label="Reverse reads" />
            </when>
            <when value="collection">
                <param format="fastq" name="reads" type="data_collection" collection_type="paired" label="Read collection" />
            </when>
        </conditional>
        <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." />
        <param name="max_overlap" argument="--max-overlap" type="integer" optional="true" value="65" label="Maximum overlap" help="Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the mismatch density is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap." />
        <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." />
        <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." />
        <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" />
    </inputs>
    <outputs>
        <data format="fastq" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads" />
        <data format="fastq" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads" />
        <data format="fastq" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads" />
        <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" />
        <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram">
            <filter>generate_histogram</filter>
        </data>
        <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)" >
            <filter>allow_outies</filter>
        </data>
        <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)" >
            <filter>allow_outies</filter>
        </data>
        <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)" >
            <filter>allow_outies and generate_histogram</filter>
        </data>
        <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)" >
            <filter>allow_outies and generate_histogram</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="forward" value="flash_forward_in1.fastq" />
            <param name="reverse" value="flash_reverse_in1.fastq" />
            <param name="generate_histogram" value="false" />
            <output name="merged_reads" file="flash_merged_out1.fastq" />
            <output name="unmerged_reads_f" file="flash_unmerged_f_out1.fastq" />
            <output name="unmerged_reads_r" file="flash_unmerged_r_out1.fastq" />
            <output name="hist" file="flash_hist_out1.tabular" />
        </test>
        <test>
            <param name="forward" value="flash_forward_in2.fastq" />
            <param name="reverse" value="flash_reverse_in2.fastq" />
            <param name="allow_outies" value="true" />
            <param name="generate_histogram" value="true" />
            <output name="merged_reads" file="flash_merged_out2.fastq" />
            <output name="unmerged_reads_f" file="flash_unmerged_f_out2.fastq" />
            <output name="unmerged_reads_r" file="flash_unmerged_r_out2.fastq" />
            <output name="hist" file="flash_hist_out2.tabular" />
            <output name="histogram" file="flash_hist_out2.txt" />
            <output name="hist_in" file="flash_hist_in_out2.tabular" />
            <output name="histogram_in" file="flash_hist_in_out2.txt" />
            <output name="hist_out" file="flash_hist_out_out2.tabular" />
            <output name="histogram_out" file="flash_hist_out_out2.txt" />
        </test>
    </tests>
    <help>
<![CDATA[
FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool

2:b48895989d78

<?xml version="1.0"?>
<tool id="flash" name="FLASH" version="@VERSION@.2">
    <description>adjust length of short reads</description>
    <macros>
        <token name="@VERSION@">1.2.11</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">flash</requirement>
    </requirements>
    <version_command>flash --version | head -n 1</version_command>
    <command detect_errors="aggressive">
        <![CDATA[
            flash --threads=\${GALAXY_SLOTS:-1}
                -m $min_overlap
                -M $max_overlap
                -x $max_mismatch_density
                $allow_outies
                #if $layout.select_layout == 'individual':
                    '$layout.forward' '$layout.reverse'
                    #set $input = $layout.forward
                #else:
                    '$layout.reads.forward' '$layout.reads.reverse'
                    #set $input = $layout.reads.forward
                #end if
                #if $input.dataset.extension == 'fastqsanger':
                    -p 33
                #else:
                    -p 64
                #end if
        ]]>
    </command>
    <inputs>
        <conditional name="layout">
            <param name="select_layout" type="select" label="Input data structure">
                <option value="individual">Individual datasets</option>
                <option value="collection">Paired collection</option>
            </param>
            <when value="individual">
                <param format="fastqsanger,fastqsolexa,fastqillumina" name="forward" type="data" label="Forward reads" />
                <param format="fastqsanger,fastqsolexa,fastqillumina" name="reverse" type="data" label="Reverse reads" />
            </when>
            <when value="collection">
                <param format="fastqsanger,fastqsolexa,fastqillumina" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
            </when>
        </conditional>
        <param name="min_overlap" argument="--min-overlap" type="integer" optional="true" value="10" label="Minimum overlap" help="The minimum required overlap length between two reads to provide a confident overlap." />
        <param name="max_overlap" argument="--max-overlap" type="integer" optional="true" value="65" label="Maximum overlap" help="Maximum overlap length expected in approximately 90% of read pairs. Overlaps longer than the maximum overlap parameter are still considered as good overlaps, but the mismatch density is calculated over the first max_overlap bases in the overlapped region rather than the entire overlap." />
        <param name="max_mismatch_density" argument="--max-mismatch-density" type="float" optional="true" value="0.25" label="Maximum mismatch density" help="Maximum allowed ratio between the number of mismatched base pairs and the overlap length. Two reads will not be combined with a given overlap if that overlap results in a mismatched base density higher than this value." />
        <param name="allow_outies" argument="--allow-outies" type="boolean" truevalue="--allow-outies" falsevalue="" checked="false" label="Combine read pairs in both orientations" help="FLASH uses the same parameters when trying each orientation. If a read pair can be combined in either orientation, the better-fitting one will be chosen using the same scoring algorithm that FLASH normally uses." />
        <param name="generate_histogram" type="boolean" truevalue="" falsevalue="" checked="false" label="Output a text rendering of the histogram" />
    </inputs>
    <outputs>
        <data format_source="reads['forward']" name="merged_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads">
            <filter>layout['select_layout'] == 'collection'</filter>
        </data>
        <data format_source="reads['forward']" name="unmerged_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads">
            <filter>layout['select_layout'] == 'collection'</filter>
        </data>
        <data format_source="reads['reverse']" name="unmerged_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads">
            <filter>layout['select_layout'] == 'collection'</filter>
        </data>
        <data format_source="forward" name="merged_paired_reads" from_work_dir="out.extendedFrags.fastq" label="${tool.name} on ${on_string}: Merged reads">
            <filter>layout['select_layout'] == 'individual'</filter>
        </data>
        <data format_source="forward" name="unmerged_paired_reads_f" from_work_dir="out.notCombined_1.fastq" label="${tool.name} on ${on_string}: Unmerged forward reads">
            <filter>layout['select_layout'] == 'individual'</filter>
        </data>
        <data format_source="reverse" name="unmerged_paired_reads_r" from_work_dir="out.notCombined_2.fastq" label="${tool.name} on ${on_string}: Unmerged reverse reads">
            <filter>layout['select_layout'] == 'individual'</filter>
        </data>
        <data format="tabular" name="hist" from_work_dir="out.hist" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram" />
        <data format="txt" name="histogram" from_work_dir="out.histogram" label="${tool.name} on ${on_string}: Unmerged reads histogram">
            <filter>generate_histogram</filter>
        </data>
        <data format="tabular" name="hist_in" from_work_dir="out.hist.innie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (in)">
            <filter>allow_outies</filter>
        </data>
        <data format="tabular" name="hist_out" from_work_dir="out.hist.outie" label="${tool.name} on ${on_string}: Unmerged reads tabular histogram (out)">
            <filter>allow_outies</filter>
        </data>
        <data format="txt" name="histogram_in" from_work_dir="out.histogram.innie" label="${tool.name} on ${on_string}: Unmerged reads histogram (in)">
            <filter>allow_outies and generate_histogram</filter>
        </data>
        <data format="txt" name="histogram_out" from_work_dir="out.histogram.outie" label="${tool.name} on ${on_string}: Unmerged reads histogram (out)">
            <filter>allow_outies and generate_histogram</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="select_layout" value="individual" />
            <param name="forward" value="flash_forward_in1.fastqsanger" ftype="fastqsanger" />
            <param name="reverse" value="flash_reverse_in1.fastqsanger" ftype="fastqsanger" />
            <param name="generate_histogram" value="false" />
            <output name="merged_paired_reads" file="flash_merged_out1.fastqsanger" ftype="fastqsanger" />
            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out1.fastqsanger" ftype="fastqsanger" />
            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out1.fastqsanger" ftype="fastqsanger" />
            <output name="hist" file="flash_hist_out1.tabular" />
        </test>
        <test>
            <param name="select_layout" value="individual" />
            <param name="forward" value="flash_forward_in2.fastqsanger" ftype="fastqsanger" />
            <param name="reverse" value="flash_reverse_in2.fastqsanger" ftype="fastqsanger" />
            <param name="allow_outies" value="true" />
            <param name="generate_histogram" value="true" />
            <output name="merged_paired_reads" file="flash_merged_out2.fastqsanger" ftype="fastqsanger" />
            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out2.fastqsanger" ftype="fastqsanger" />
            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out2.fastqsanger" ftype="fastqsanger" />
            <output name="hist" file="flash_hist_out2.tabular" />
            <output name="histogram" file="flash_hist_out2.txt" />
            <output name="hist_in" file="flash_hist_in_out2.tabular" />
            <output name="histogram_in" file="flash_hist_in_out2.txt" />
            <output name="hist_out" file="flash_hist_out_out2.tabular" />
            <output name="histogram_out" file="flash_hist_out_out2.txt" />
        </test>
        <test>
            <param name="select_layout" value="collection" />
            <param name="generate_histogram" value="false" />
            <param name="reads">
                <collection type="paired">
                    <element name="forward" value="flash_forward_in3.fastqillumina" ftype="fastqillumina" />
                    <element name="reverse" value="flash_reverse_in3.fastqillumina" ftype="fastqillumina" />
                </collection>
            </param>
            <output name="merged_reads" file="flash_merged_out3.fastqillumina" ftype="fastqillumina" />
            <output name="unmerged_reads_f" file="flash_unmerged_f_out3.fastqillumina" ftype="fastqillumina" />
            <output name="unmerged_reads_r" file="flash_unmerged_r_out3.fastqillumina" ftype="fastqillumina" />
            <output name="hist" file="flash_hist_out3.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool