comparison segalign.xml @ 8:150de8a3954a draft

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/segalign commit 11132ef8b4103731b6f5860ea736bf332a06e303

7:39c21be8f8b9

        <import>system_options.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <required_files>
        <include path="diagonal_partition.py"/>
        <include path="lastz-cmd.ini"/>
        <include path="package_output.py"/>
        <include path="run_segalign_diagonal_partition"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
##
## https://www.gnu.org/software/coreutils/manual/html_node/nproc-invocation.html
##

#if str($mode.mode_selector) == "segalign"
    #if str($mode.diagonal_partition_options.diagonal_partition) == "true"
        #set $segalign_mode = "segalign_diagonal_partition"
        ## explicitly calling bash to bypass a pulsar bug
        ## https://github.com/galaxyproject/pulsar/issues/341
        bash '$__tool_directory__/run_segalign_diagonal_partition'
            --tool_directory '$__tool_directory__'
            --max_segments '$mode.diagonal_partition_options.max_segments'
    #else
        #set $segalign_mode = "segalign"
        run_segalign
    #end if
            '$mode.target'
            '$mode.query'
#else if str($mode.mode_selector) == "segalign_repeat_masker"
    #set $segalign_mode = "segalign_repeat_masker"

                    <expand macro="segalign_output_options"/>
                </expand>
                <expand macro="system_options"/>
                <section name="diagonal_partition_options" expanded="false" title="Diagonal Partition Options">
                    <param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization"/>
                    <param argument="--max_segments" type="integer" value="20000" label="Max segments"/>
                </section>
            </when>
            <when value="segalign_repeat_masker">
                <param name="seq_file" type="data" format="fasta,fasta.gz" label="Sequence file in FASTA format"/>
                <expand macro="sequence_options">

8:150de8a3954a

        <import>system_options.xml</import>
    </macros>
    <expand macro="edam_ontology"/>
    <expand macro="requirements"/>
    <required_files>
        <include path="lastz-cmd.ini"/>
        <include path="package_output.py"/>
        <include path="runner.py"/>
    </required_files>
    <command detect_errors="exit_code"><![CDATA[
##
## https://www.gnu.org/software/coreutils/manual/html_node/nproc-invocation.html
##

#if str($mode.mode_selector) == "segalign"
    #if str($mode.diagonal_partition_options.diagonal_partition) == "true"
        #set $segalign_mode = "segalign_diagonal_partition"
        ## explicitly calling bash to bypass a pulsar bug
        ## https://github.com/galaxyproject/pulsar/issues/341
        bash '$__tool_directory__/runner.py'
            --output-type tarball
            --output-filename fake
            --diagonal-partition
            --num-cpu \${GALAXY_SLOTS:-2}
            --tool_directory '$__tool_directory__'
    #else
        #set $segalign_mode = "segalign"
        bash '$__tool_directory__/runner.py'
            --output-type output
            --output-filename foo.maf
            --num-cpu \${GALAXY_SLOTS:-2}
            --tool_directory '$__tool_directory__'
    #end if
            '$mode.target'
            '$mode.query'
#else if str($mode.mode_selector) == "segalign_repeat_masker"
    #set $segalign_mode = "segalign_repeat_masker"

                    <expand macro="segalign_output_options"/>
                </expand>
                <expand macro="system_options"/>
                <section name="diagonal_partition_options" expanded="false" title="Diagonal Partition Options">
                    <param argument="--diagonal_partition" type="boolean" value="false" label="Enable diagonal partition optimization"/>
                </section>
            </when>
            <when value="segalign_repeat_masker">
                <param name="seq_file" type="data" format="fasta,fasta.gz" label="Sequence file in FASTA format"/>
                <expand macro="sequence_options">