comparison hyphy_summary.xml @ 3:bd90215b7d15 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ec5db8349483b2cd46f9da23abe6cefcf65bc714"

2:d7c01f81739b

<?xml version="1.0"?>
<tool id="hyphy_summary" version="1.1.0" name="HyPhy-Summary" profile="21.01">
    <description>generate summary report of HyPhy analyses</description>
    <requirements>
        <requirement type="package" version="0.19.7">python-bioext</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/scripts/hyphy_summary.py' 
            --mode $mode_conditional.mode
            #if $mode_conditional.mode == 'summary':

                <param argument="--fel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-FEL output dataset" />
                <param argument="--cfel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-CFEL output dataset" />
                <param argument="--bgm" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-BGM output dataset" />
            </when>
            <when value="merge">
                <param argument="--summary-inputs" type="data" format="hyphy_results.json" multiple="true" label="Segment annotations to merge" />
                <param argument="--annotation-inputs" type="data" format="hyphy_results.json" multiple="true" label="Site annotations to merge" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="summary" format="hyphy_results.json" label="${tool.name} on ${on_string} - Segment annotations" />
        <data name="annotation" format="hyphy_results.json" label="${tool.name} on ${on_string} - Site annotations" />
    </outputs>
    <tests>
        <test>
            <param name="mode" value="summary" />
            <param name="name" value="epi_isl_1009769" />
            <param name="gene" value="nsp8" />
            <param name="combined" value="summary/nsp8.combined.fas" />
            <param name="fade" value="summary/nsp8.FADE.json" />
            <param name="prime" value="summary/nsp8.PRIME.json" />
            <param name="relax" value="summary/nsp8.RELAX.json" />

            <output name="summary" file="summary/nsp8-segment.json" />
            <output name="annotation" file="summary/nsp8-site.json" />
        </test>
        <test>
            <param name="mode" value="summary" />
            <param name="name" value="epi_isl_1009769" />
            <param name="gene" value="ORF6" />
            <param name="combined" value="summary/ORF6.combined.fas" />
            <param name="fade" value="summary/ORF6.FADE.json" />
            <param name="meme_full" value="summary/ORF6.MEME-full.json" />
            <param name="labels" value="summary/ORF6.labels.json" />

            <output name="summary" file="summary/ORF6-segment.json" />
            <output name="annotation" file="summary/ORF6-site.json" />
        </test>
        <test>
            <param name="mode" value="summary" />
            <param name="name" value="epi_isl_1009769" />
            <param name="gene" value="nsp7" />
            <param name="combined" value="summary/nsp7.combined.fas" />
            <param name="fade" value="summary/nsp7.FADE.json" />
            <param name="meme_full" value="summary/nsp7.MEME-full.json" />
            <param name="labels" value="summary/nsp7.labels.json" />

3:bd90215b7d15

<?xml version="1.0"?>
<tool id="hyphy_summary" version="1.2.0" name="HyPhy-Summary" profile="21.01">
    <description>generate summary report of HyPhy analyses</description>
    <requirements>
        <requirement type="package" version="0.20.1">python-bioext</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        python '$__tool_directory__/scripts/hyphy_summary.py' 
            --mode $mode_conditional.mode
            #if $mode_conditional.mode == 'summary':

                <param argument="--fel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-FEL output dataset" />
                <param argument="--cfel" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-CFEL output dataset" />
                <param argument="--bgm" type="data" format="json,hyphy_results.json" optional="true" label="HyPhy-BGM output dataset" />
            </when>
            <when value="merge">
                <param argument="--summary-inputs" type="data" format="hyphy_results.json" multiple="true" label="Summaries to merge" />
                <param argument="--annotation-inputs" type="data" format="hyphy_results.json" multiple="true" label="Annotations to merge" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="summary" format="hyphy_results.json" label="${tool.name} on ${on_string} - Summary" />
        <data name="annotation" format="hyphy_results.json" label="${tool.name} on ${on_string} - Annotation" />
    </outputs>
    <tests>
        <test>
            <param name="mode" value="summary" />
            <param name="name" value="REFERENCE" />
            <param name="gene" value="nsp8" />
            <param name="combined" value="summary/nsp8.combined.fas" />
            <param name="fade" value="summary/nsp8.FADE.json" />
            <param name="prime" value="summary/nsp8.PRIME.json" />
            <param name="relax" value="summary/nsp8.RELAX.json" />

            <output name="summary" file="summary/nsp8-segment.json" />
            <output name="annotation" file="summary/nsp8-site.json" />
        </test>
        <test>
            <param name="mode" value="summary" />
            <param name="name" value="REFERENCE" />
            <param name="gene" value="ORF6" />
            <param name="combined" value="summary/ORF6.combined.fas" />
            <param name="fade" value="summary/ORF6.FADE.json" />
            <param name="meme_full" value="summary/ORF6.MEME-full.json" />
            <param name="labels" value="summary/ORF6.labels.json" />

            <output name="summary" file="summary/ORF6-segment.json" />
            <output name="annotation" file="summary/ORF6-site.json" />
        </test>
        <test>
            <param name="mode" value="summary" />
            <param name="name" value="REFERENCE" />
            <param name="gene" value="nsp7" />
            <param name="combined" value="summary/nsp7.combined.fas" />
            <param name="fade" value="summary/nsp7.FADE.json" />
            <param name="meme_full" value="summary/nsp7.MEME-full.json" />
            <param name="labels" value="summary/nsp7.labels.json" />