comparison medaka_consensus.xml @ 3:35666d44fe7a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e80b649094384fc6d7a8f917300db3550cc99a44"

2:6a87478ed985

<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"/>

-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"/>

                    <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/>
                </assert_contents>
            </output>
            <output name="out_probs">
                <assert_contents>
                    <has_size value="192187" delta="100"/>
                </assert_contents>
            </output>
            <output name="out_calls">
                <assert_contents>
                    <has_size value="533242" delta="100"/>
                </assert_contents>
            </output>
        </test>
        <!-- #2 -->
        <test expect_num_outputs="7">

            <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/>
            <output name="out_consensus">
                <assert_contents>
                    <has_n_lines n="65"/>
                    <has_line line=">4 length=3792 depth=114.52x circular=true"/>
                    <has_line line="CATCTCTTT"/>
                </assert_contents>
            </output>
            <output name="out_probs">
                <assert_contents>
                    <has_size value="192710" delta="100"/>
                </assert_contents>
            </output>
            <output name="out_calls">
                <assert_contents>
                    <has_size value="533163" delta="100"/>
                </assert_contents>
            </output>
            <output name="out_draft">
                <assert_contents>
                    <has_n_lines n="6"/>
                    <has_line line="chain 3789 4 3792 + 0 3792 4 3789 + 0 3789 1"/>
                    <has_line line="1204"/>
                </assert_contents>
            </output>
            <output name="out_polished">
                <assert_contents>
                    <has_size value="9"/>

3:35666d44fe7a

<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
    <description>Assembly polishing via neural networks</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

-t \${GALAXY_SLOTS:-4}
## required
-i '$i'
-d '$d'

2>&1 | 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"/>

                    <has_text_matching expression=".+GTCAGAATCGCGTTCAGCGCGTTTCAGCGGTGCGTACAATT.+"/>
                </assert_contents>
            </output>
            <output name="out_probs">
                <assert_contents>
                    <!-- <has_size value="192187" delta="100"/> -->
                    <has_size value="165271" delta="100"/>
                </assert_contents>
            </output>
            <output name="out_calls">
                <assert_contents>
                    <!-- <has_size value="533242" delta="100"/> -->
                    <has_size value="343197" delta="100"/>
                </assert_contents>
            </output>
        </test>
        <!-- #2 -->
        <test expect_num_outputs="7">

            <param name="out" value="consensus,probs,calls,draft,variants,polished,log"/>
            <output name="out_consensus">
                <assert_contents>
                    <has_n_lines n="65"/>
                    <has_line line=">4 length=3792 depth=114.52x circular=true"/>
                    <has_line line="ATCTCTTT"/>
                </assert_contents>
            </output>
            <output name="out_probs">
                <assert_contents>
                    <has_size value="166251" delta="100"/>
                    <!-- <has_size value="192710" delta="100"/> -->
                </assert_contents>
            </output>
            <output name="out_calls">
                <assert_contents>
                    <has_size value="343197" delta="100"/>
                    <!-- <has_size value="533163" delta="100"/> -->
                </assert_contents>
            </output>
            <output name="out_draft">
                <assert_contents>
                    <has_line line="chain 3788 4 3792 + 0 3792 4 3788 + 0 3788 1"/>
                    <has_line line="1409 1 0"/>
                    <has_line line="440 1 0"/>
                    <has_line line="736 1 0"/>
                    <has_line line="853 1 0"/>
                    <has_line line="350"/>
                </assert_contents>
            </output>
            <output name="out_polished">
                <assert_contents>
                    <has_size value="9"/>