comparison coverm_contig.xml @ 1:688a777e1b19 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112

0:6941d0d453ba

<tool id="coverm_contig" name="CoverM-CONTIG" version="@TOOL_VERSION@" python_template_version="3.5">
    <macros>
        <import>macros.xml</import>
        <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
        <token name="@TOOL_VERSION@">0.2.1</token>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
         #if $reads.read_type == "single" or $reads.read_type == "interleaved"
            mkdir -p reads1 &&

                --min-covered-fraction $cov.min_covered_fraction
            #end if
            #if $cov.contig_end_exclusion:
                --contig-end-exclusion $cov.contig_end_exclusion
            #end if
            #if $cov.cond_methods.trimmed_mean
                #if $cov.cond_methods.trim_min:
                    --trim-min $cov.cond_methods.trim_min
                #end if
                #if $cov.cond_methods.trim_max:
                    --trim_max $cov.cond_methods.trim_max

            #if $out.output_format:
                --output-format $out.output_format
            #end if
            --output-file output.tsv
            --threads \${GALAXY_SLOTS:-1}
            2> stdout.txt
    ]]></command>
    <inputs>
        <expand macro="reads_for_contig" />
        <expand macro="add_reads" />
        <section name="shar" title="Sharding" expanded="false">

1:688a777e1b19

<tool id="coverm_contig" name="CoverM contig" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Calculate coverage of individual contigs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command><![CDATA[
         #if $reads.read_type == "single" or $reads.read_type == "interleaved"
            mkdir -p reads1 &&

                --min-covered-fraction $cov.min_covered_fraction
            #end if
            #if $cov.contig_end_exclusion:
                --contig-end-exclusion $cov.contig_end_exclusion
            #end if
            #if $cov.cond_methods.trimmed_mean == "trimmed_mean"
                #if $cov.cond_methods.trim_min:
                    --trim-min $cov.cond_methods.trim_min
                #end if
                #if $cov.cond_methods.trim_max:
                    --trim_max $cov.cond_methods.trim_max

            #if $out.output_format:
                --output-format $out.output_format
            #end if
            --output-file output.tsv
            --threads \${GALAXY_SLOTS:-1}
    ]]></command>
    <inputs>
        <expand macro="reads_for_contig" />
        <expand macro="add_reads" />
        <section name="shar" title="Sharding" expanded="false">