view seqkit_head.xml @ 2:6fb76225bdb1 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 89cc1cb215aa5dc5ef6364bf13bbb1978367dce3

<tool id="seqkit_head" name="SeqKit Head" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Displays N records of a FASTA or FASTQ file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="exit_code"><![CDATA[
        #set $input_fn='input.' + str($input.ext)
        #set $output_fn='seqkithead_output.' + str($output.ext)
        ln -s '$input' '$input_fn'
        && seqkit head
        '$input_fn'
        --number '$number'
        -o '$output_fn'
        --threads \${GALAXY_SLOTS:-4}

]]></command>
    <inputs>
        <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
        <param argument="--number" type="integer" value="10" label="Output first N FASTA/Q records"/>
    </inputs>
    <outputs>
        <data name="output" format_source="input" from_work_dir="seqkithead_output.*" label="${input.name} Head (${tool.name})"/>
    </outputs>
    <tests>
        <!-- 1. fastq.gz -->
        <test expect_num_outputs="1">
            <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
            <param name="number" value="10"/>
            <output name="output" file="head_output1.fastq.gz" ftype="fastqsanger.gz"/>
        </test>
        <!-- 2. fasta.gz -->
        <test expect_num_outputs="1">
            <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
            <param name="number" value="10"/>
            <output name="output" file="head_output2.fasta.gz" ftype="fasta.gz"/>
        </test>
    </tests>
    <help>
**What it does**

Prints first N FASTA/Q records,

    </help>
    <expand macro="citations"/>
</tool>