annotate assembly-stats.xml @ 0:9e4955725212 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/assembly-stats commit 28119c39c4b59a67f629c8ca569d58f4d2949c9c

<?xml version="1.0"?>
<tool id="assembly_stats" name="Assembly stats" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>visualisations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">rjchallis-assembly-stats</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if $output_format == "html"
            SRC="\$(dirname \$(which asm2stats.pl))/../opt/assembly-stats" &&
            mkdir -p $output.files_path &&
            
            cp -r "\$SRC/css/" '$output.files_path'  &&
            cp -r "\$SRC/js/" '$output.files_path'  &&
            cp '$__tool_directory__/d3-tip.js' '${output.files_path}/js/d3-tip.js' && 
            mkdir -p '$output.files_path/json/' &&
            cp '$__tool_directory__/assembly-stats.html' '$output' && 
            cp '$__tool_directory__/assembly-stats.html' '${output.files_path}' && 

            asm2stats.minmaxgc.pl '${input_fasta}' > '${output.files_path}/json/output.assembly-stats.json' ######
        #else
            asm2stats.minmaxgc.pl '${input_fasta}' > '${output}'
        #end if

    ]]></command>

    <inputs>
        <param name="input_fasta" type="data" format="fasta" label="Genome assembly"/>
        <param name="output_format" type="select" label="Output format" >
            <option value="html" selected="true">HTML</option>
            <option value="json">JSON</option>
        </param>
    </inputs>
    
    <outputs>
        <data name="output" format="html" label="Assembly-stats on ${on_string}" >
            <change_format>
                <when input="output_format" value="json" format="json" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sequence.fasta"/>
            <param name="output_format" value="json"/>
            <output name="output" ftype="json">
                <assert_contents>
                    <has_text text='"contig_count" : 1' />
                    <has_text text='"scaffold_count" : 1' />
                    <has_text text='154478' />
                    <has_text text='"GC" : 36.29' />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <param name="input_fasta" value="sequence.fasta"/>
            <param name="output_format" value="html"/>
            <output name="output" value="assembly-stats.html" ftype="html">
                <assert_contents>
                    <has_size value="7819"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    
    <help><![CDATA[
        assembly_stats_ Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality.

        .. _assembly_stats: https://github.com/rjchallis/assembly-stats
    ]]></help>
    <expand macro="citation"/>
</tool>