comparison hicup_hicup.xml @ 2:e96cb39c3f8e draft

planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit c546c919808a853d3e1556cb28bb4a5f7e1f9932

1:b191af7e2476

<tool id="hicup_hicup" name="Hicup Pipeline" version="0.1.0">
    <description>controls the other programs in the HiCUP pipeline.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />

        <expand macro="re1" />
        <expand macro="reference_genome_macro" />
        <section name="advanced_options" title="Advanced options">
            <expand macro="re2" />
            <expand macro="filter_longest_shortest" />
            <expand macro="no_fill" />     
        </section>
    </inputs>
    <outputs>
        <!-- Regular output of hicup -->
        <data name="hicup_results" format="html" from_work_dir="results.html" label="HiCUP results"/>

                <param name="own_file" value="chr1.fa"/>
            </conditional>

            <!-- outputs -->
            <output name="hicup_results" file="results.html" ftype="html" lines_diff="10000"/>
            <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="5" />
            <output name="hicup_report" file="HiCUP_summary_report.txt" lines_diff="2"/>
            
            <output_collection name="intermediate_results">
                <!-- truncater step-->
                <element name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/>

2:e96cb39c3f8e

<tool id="hicup_hicup" name="Hicup Pipeline" version="@VERSION@.0">
    <description>controls the other programs in the HiCUP pipeline.</description>
    <macros>
        <import>hicup_macros.xml</import>
    </macros>
    <expand macro="requirements_hicup" />

        <expand macro="re1" />
        <expand macro="reference_genome_macro" />
        <section name="advanced_options" title="Advanced options">
            <expand macro="re2" />
            <expand macro="filter_longest_shortest" />
            <expand macro="no_fill" />
        </section>
    </inputs>
    <outputs>
        <!-- Regular output of hicup -->
        <data name="hicup_results" format="html" from_work_dir="results.html" label="HiCUP results"/>

                <param name="own_file" value="chr1.fa"/>
            </conditional>

            <!-- outputs -->
            <output name="hicup_results" file="results.html" ftype="html" lines_diff="10000"/>
            <output name="dataset_hicup" file="dataset.hicup.sam" lines_diff="10" />
            <output name="hicup_report" file="HiCUP_summary_report.txt" lines_diff="2"/>
            
            <output_collection name="intermediate_results">
                <!-- truncater step-->
                <element name="hicup_truncater_summary" file="hicup_truncater_summary.txt" lines_diff="8"/>