comparison humann2.xml @ 6:cda49fede0c2 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 8d953926efdf23d8c3fb8719341dff51a55a92f2"

5:bb13650e8115

<tool id="humann2" name="HUMAnN2" version="@WRAPPER_VERSION@.2">
    <description>to profile presence/absence and abundance of microbial pathways and gene families</description>
    <macros>
        <import>humann2_macros.xml</import>
    </macros>
    <expand macro="stdio"/>

            --pkl_output 'ref_db/metadata.pkl'
        &&
    #end if
#end if

humann2
    --input '$input'
    -o 'output'
    $bypass.bypass_prescreen
    $bypass.bypass_nucleotide_index
    $bypass.bypass_translated_search
    $bypass.bypass_nucleotide_search

    --output-basename 'humann2'
    $adv.remove_statified_output
    $adv.remove_column_description_output
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="fastq,fasta,sam,bam,biom1" label="Input sequence file"/>
        <section name="bypass" title="Options to bypass some steps" expanded="False">
            <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" truevalue="--bypass-prescreen" falsevalue="" checked="false" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
            <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" truevalue="--bypass-nucleotide-index" falsevalue="" checked="false" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
            <param name="bypass_translated_search" argument="--bypass-translated-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the translated search step?"/>
            <param name="bypass_nucleotide_search" argument="--bypass-nucleotide-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the nucleotide search steps?"/>

                    <has_text text="UNINTEGRATED" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="input_sequences.fasta"/>
            <param name="bypass_prescreen" value=""/>
            <param name="bypass_nucleotide_index" value=""/>
            <param name="bypass_translated_search" value=""/>
            <param name="bypass_nucleotide_search" value=""/>
            <param name="nucleotide_db_selector" value="history"/>

6:cda49fede0c2

<tool id="humann2" name="HUMAnN2" version="@WRAPPER_VERSION@.3">
    <description>to profile presence/absence and abundance of microbial pathways and gene families</description>
    <macros>
        <import>humann2_macros.xml</import>
    </macros>
    <expand macro="stdio"/>

            --pkl_output 'ref_db/metadata.pkl'
        &&
    #end if
#end if

#if $input.ext.startswith("fasta")
    #set ext="fasta"
#else if $input.ext.startswith("fastq")
    #set ext="fastq"
#else if $input.ext.endswith("bam")
    #set ext="bam"
#else if $input.ext == 'sam'
    #set ext="sam"
#else if $input.ext == 'biom1'
    #set ext="biom"
#else
    >&2 "unknown extension $input.ext"
    exit 1; 
#end if

#if $input.ext.endswith(".gz")
    #set ext+=".gz"
#end if

humann2
    --input '$input'
    --input-format $ext
    -o 'output'
    $bypass.bypass_prescreen
    $bypass.bypass_nucleotide_index
    $bypass.bypass_translated_search
    $bypass.bypass_nucleotide_search

    --output-basename 'humann2'
    $adv.remove_statified_output
    $adv.remove_column_description_output
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="fastq,fastq.gz,fasta,fasta.gz,sam,bam,biom1" label="Input sequence file"/>
        <section name="bypass" title="Options to bypass some steps" expanded="False">
            <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" truevalue="--bypass-prescreen" falsevalue="" checked="false" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
            <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" truevalue="--bypass-nucleotide-index" falsevalue="" checked="false" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
            <param name="bypass_translated_search" argument="--bypass-translated-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the translated search step?"/>
            <param name="bypass_nucleotide_search" argument="--bypass-nucleotide-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the nucleotide search steps?"/>

                    <has_text text="UNINTEGRATED" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input" value="input_sequences.fastq.gz"/>
            <param name="bypass_prescreen" value=""/>
            <param name="bypass_nucleotide_index" value=""/>
            <param name="bypass_translated_search" value=""/>
            <param name="bypass_nucleotide_search" value=""/>
            <param name="nucleotide_db_selector" value="history"/>