comparison medaka_consensus.xml @ 1:551f8c9bc4cf draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"

0:ef94bace3a3c

<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
    <description>Assembly polishing via neural networks</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
        medaka_consensus
        ## optional
        -m '${m}'
        -b $b
        -o 'results'
        #if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',')
            -v
        #end if
        -t \${GALAXY_SLOTS:-4}
        ## required
        -i '$i'
        -d '$d'

        |& tee 'log.txt'
        #if 'variants' in str($out).split(',')
            && bgzip -d 'results/variants.vcf.gz'
        #end if
    ]]></command>
    <inputs>
        <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/>
        <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/>
        <expand macro="model"/>

        </data>
        <!-- optional with parameter -v -->
        <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus">
            <filter>'draft' in out</filter>
        </data>
        <data name="out_variants" format="vcf" from_work_dir="results/variants.vcf" label="${tool.name} on ${on_string}: Variants">
            <filter>'variants' in out</filter>
        </data>
        <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft">
            <filter>'polished' in out</filter>
        </data>
        <!-- optional -->
        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
            <filter>'log' in out</filter>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->

            <output name="out_polished">
                <assert_contents>
                    <has_size value="9"/>
                </assert_contents>
            </output>
            <output name="out_variants">
                <assert_contents>
                    <has_n_lines n="9"/>
                    <has_line line="##fileformat=VCFv4.1"/>
                    <has_text_matching expression="4&#009;.+"/>
                </assert_contents>
            </output>
            <output name="out_log">
                <assert_contents>
                    <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/>
                </assert_contents>
            </output>

1:551f8c9bc4cf

<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
    <description>Assembly polishing via neural networks</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="exit_code"><![CDATA[
medaka_consensus
## optional
-m ${m}
-b $b
-o results
#if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',')
    -v
#end if
-t \${GALAXY_SLOTS:-4}
## required
-i '$i'
-d '$d'

|& tee '$out_log'
    ]]></command>
    <inputs>
        <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/>
        <param argument="-d" type="data" format="fasta,fasta.gz" label="Select assembly" help="The input assembly should be preprocessed with racon."/>
        <expand macro="model"/>

        </data>
        <!-- optional with parameter -v -->
        <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus">
            <filter>'draft' in out</filter>
        </data>
        <data name="out_variants" format="vcf_bgzip" from_work_dir="results/variants.vcf.gz" label="${tool.name} on ${on_string}: Variants">
            <filter>'variants' in out</filter>
        </data>
        <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft">
            <filter>'polished' in out</filter>
        </data>
        <!-- optional -->
        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
            <filter>'log' in out</filter>
        </data>
    </outputs>
    <tests>
        <!-- #1 default -->

            <output name="out_polished">
                <assert_contents>
                    <has_size value="9"/>
                </assert_contents>
            </output>
            <output name="out_variants" file="variants.vcf.gz" decompress="true"/>
            <output name="out_log">
                <assert_contents>
                    <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/>
                </assert_contents>
            </output>