comparison hicup_macros.xml @ 3:7e21a0b8d48c draft

planemo upload for repository https://github.com/joachimwolff/galaxytools/tree/hicup/tools/hicup commit e6a9507eb198c6bf2c63ddae387c262bfc8dbd16

2:e525d4f051b9

        <stdio>
            <exit_code range="1:" />
        </stdio>
    </xml>
    <xml name="citation_hicup">
       <citations>
	        <citation type="doi">10.12688/f1000research.7334.1</citation>
	    </citations>  
    </xml>
    <xml name="reference_genome_macro">
        <conditional name="reference_genome">
            <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
                <option value="indexed">Use a built-in genome index</option>
                <option value="history">Use a genome from the history and build index</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                <options from_data_table="bowtie2_indices">
                    <filter type="sort_by" column="2"/>
                    <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                </options>
                </param>
            </when>

        <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary.txt" />
        <data name="dataset1_trunc" format="fastq" label="Hicup Dataset1 Truncation" from_work_dir="dataset1.trunc.fastq" />
        <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" />
        <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" />
        <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" />
        
    </xml>
    <xml name="input_files">
        <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/>
        <param name="input_second_sequence" type="data" format="fastq" label="Second input sequence" help="The second sequence:"/>
    </xml>

3:7e21a0b8d48c

        <stdio>
            <exit_code range="1:" />
        </stdio>
    </xml>
    <xml name="citation_hicup">
	<citations>
        <citation type="doi">10.12688/f1000research.7334.1</citation>
	</citations>  
    </xml>
    <xml name="reference_genome_macro">
        <conditional name="reference_genome">
            <param name="source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options. See `Indexes` section of help below">
                <option value="indexed">Use a built-in genome index</option>
                <option value="history">Use a genome from the history and build index</option>
            </param>
            <when value="indexed">
                <param name="index" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
                <options from_data_table="bowtie2_indexes">
                    <filter type="sort_by" column="2"/>
                    <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                </options>
                </param>
            </when>

        <data name="hicup_truncater_summary" format="txt" label="hicup_truncater_summary.txt" from_work_dir="hicup_truncater_summary.txt" />
        <data name="dataset1_trunc" format="fastq" label="Hicup Dataset1 Truncation" from_work_dir="dataset1.trunc.fastq" />
        <data name="dataset2_trunc" format="fastq" label="Hicup Dataset2 Truncation" from_work_dir="dataset2.trunc.fastq" />
        <data name="dataset1_truncater_barchart" format="svg" label="Hicup Dataset1 Truncation Barchart.svg" from_work_dir="dataset1.truncation_barchart.svg" />
        <data name="dataset2_truncater_barchart" format="svg" label="Hicup Dataset2 Truncation Barchart.svg" from_work_dir="dataset2.truncation_barchart.svg" />
    </xml>
    <xml name="input_files">
        <param name="input_first_sequence" type="data" format="fastq" label="First input sequence" help="The first sequence:"/>
        <param name="input_second_sequence" type="data" format="fastq" label="Second input sequence" help="The second sequence:"/>
    </xml>