comparison flash.xml @ 5:a27654fc4270 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flash commit 5b2c074b4f1586dbf20f42603e36d1d50460fd31

4:c85bdba47254

<?xml version="1.0"?>
<tool id="flash" name="FLASH" version="@VERSION@.3">
    <description>adjust length of short reads</description>
    <macros>
        <token name="@VERSION@">1.2.11</token>
    </macros>
    <requirements>

                    #set $input = $layout.forward
                #else:
                    '$layout.reads.forward' '$layout.reads.reverse'
                    #set $input = $layout.reads.forward
                #end if
                #if $input.is_of_type('fastqsanger'):
                    -p 33
                #else:
                    -p 64
                #end if

                #if $save_log:
                    > '$log'
                #end if
        ]]>
    </command>

            <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>
            <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

5:a27654fc4270

<?xml version="1.0"?>
<tool id="flash" name="FLASH" version="@VERSION@.4">
    <description>adjust length of short reads</description>
    <macros>
        <token name="@VERSION@">1.2.11</token>
    </macros>
    <requirements>

                    #set $input = $layout.forward
                #else:
                    '$layout.reads.forward' '$layout.reads.reverse'
                    #set $input = $layout.reads.forward
                #end if
                #if $input.is_of_type('fastqsanger', 'fastqsanger.gz'):
                    -p 33
                #else:
                    -p 64
                #end if
                #if $input.ext.endswith('.gz'):
                    -z
                #end if
                --output-suffix=''
                #if $save_log:
                    > '$log'
                #end if
        ]]>
    </command>

            <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,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="forward" type="data" label="Forward reads" />
                <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" name="reverse" type="data" label="Reverse reads" />
            </when>
            <when value="collection">
                <param format="fastqsanger,fastqsolexa,fastqillumina,fastqsanger.gz,fastqsolexa.gz,fastqillumina.gz" 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>
            <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>
        <test>
            <param name="select_layout" value="individual" />
            <param name="forward" value="flash_forward_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
            <param name="reverse" value="flash_reverse_in4.fastqsanger.gz" ftype="fastqsanger.gz" />
            <param name="generate_histogram" value="false" />
            <param name="save_log" value="true" />
            <output name="merged_paired_reads" file="flash_merged_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
            <output name="unmerged_paired_reads_f" file="flash_unmerged_f_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
            <output name="unmerged_paired_reads_r" file="flash_unmerged_r_out4.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
            <output name="log">
              <assert_contents>
                <has_line_matching expression=".*Percent combined: 3.60%" />
              </assert_contents>
            </output>
        </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_in5.fastqsanger.gz" ftype="fastqsanger.gz" />
                    <element name="reverse" value="flash_reverse_in5.fastqsanger.gz" ftype="fastqsanger.gz" />
                </collection>
            </param>
            <output name="merged_reads" file="flash_merged_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
            <output name="unmerged_reads_f" file="flash_unmerged_f_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
            <output name="unmerged_reads_r" file="flash_unmerged_r_out5.fastqsanger.gz" ftype="fastqsanger.gz" compare="sim_size" />
            <output name="hist" file="flash_hist_out5.tabular" />
        </test>
    </tests>
    <help>
<![CDATA[
FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool