comparison meryl.xml @ 11:29dabd8db6f2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit e479a44b3c6e7a3c0facdb325892b0a6da6f0cd2

10:9cd178127b19

                mkdir 'child${i}.meryl' &&
                ln -s '$read' ./input_child_${i}.${read.ext} &&
                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' &&
            #end for
            meryl union-sum child*.meryl output child.meryl &&
            ## mat specific kmers
            meryl difference mat.meryl pat.meryl output mat.only.meryl &&
            meryl histogram mat.only.meryl > mat.only.hist &&
            java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy &&
            VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` &&

            java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy &&
            VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` &&
            meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl &&
            tar -czf 'pat.meryldb' pat.hapmer.meryl &&

            ## shared hapmers
            meryl intersect output shared.inherited.meryl child.meryl shared.meryl &&
            meryl histogram shared.inherited.meryl > shared.inherited.hist &&
            java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar shared.inherited.hist > shared.inherited.ploidy &&
            VAR=`sed -n 2p shared.inherited.ploidy | awk '{print \$NF}'` &&
            meryl greater-than \$VAR output shared.filt.meryl shared.inherited.meryl &&
            
            ## child hapmers
            meryl union-sum output child.inherited.meryl mat.inherited.meryl pat.inherited.meryl shared.inherited.meryl &&
            meryl difference output read.only.meryl child.meryl child.inherited.meryl &&
            tar -czf 'read-db.meryldb' read.only.meryl &&
            echo 'K-mer size: ${size}'
        #end if
    ]]>    </command>
    <inputs>
        <conditional name="operation_type">

                <param name="child_reads" value="child.fasta" />
                <param name="paternal_reads" value="paternal.fasta" />
                <param name="maternal_reads" value="maternal.fasta" />
                <conditional name="options_kmer_size">
                    <param name="kmer_size" value="provide" />
                    <param name="input_kmer_size" value="7" />
                </conditional>
            </conditional>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="1573" delta="300" />
                </assert_contents>
            </output>
            <output name="read_db_hist" file="output_23.read-db.hist" />
            <output name="pat_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="1779" delta="300" />
                </assert_contents>
            </output>
            <output name="pat_db_hist" file="output_23.pat.hist" />
            <output name="mat_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="1569" delta="300" />
                </assert_contents>
            </output>
            <output name="mat_db_hist" file="output_23.mat.hist" />
        </test>
        <test expect_num_outputs="1">

11:29dabd8db6f2

                mkdir 'child${i}.meryl' &&
                ln -s '$read' ./input_child_${i}.${read.ext} &&
                meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' &&
            #end for
            meryl union-sum child*.meryl output child.meryl &&
            meryl histogram child.meryl > read-db.hist &&                                          
            tar -czf 'read-db.meryldb' child.meryl &&
            
            ## mat specific kmers
            meryl difference mat.meryl pat.meryl output mat.only.meryl &&
            meryl histogram mat.only.meryl > mat.only.hist &&
            java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar mat.only.hist > mat.only.ploidy &&
            VAR=`sed -n 2p mat.only.ploidy | awk '{print \$NF}'` &&

            java -jar -Xmx1g \$MERQURY/eval/kmerHistToPloidyDepth.jar pat.inherited.hist > pat.inherited.ploidy &&
            VAR=`sed -n 2p pat.inherited.ploidy | awk '{print \$NF}'` &&
            meryl greater-than \$VAR output pat.hapmer.meryl pat.inherited.meryl &&
            tar -czf 'pat.meryldb' pat.hapmer.meryl &&

            echo 'K-mer size: ${size}'
        #end if
    ]]>    </command>
    <inputs>
        <conditional name="operation_type">

                <param name="child_reads" value="child.fasta" />
                <param name="paternal_reads" value="paternal.fasta" />
                <param name="maternal_reads" value="maternal.fasta" />
                <conditional name="options_kmer_size">
                    <param name="kmer_size" value="provide" />
                    <param name="input_kmer_size" value="21" />
                </conditional>
            </conditional>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="3362942" delta="300" />
                </assert_contents>
            </output>
            <output name="read_db_hist" file="output_23.read-db.hist" />
            <output name="pat_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="120610" delta="300" />
                </assert_contents>
            </output>
            <output name="pat_db_hist" file="output_23.pat.hist" />
            <output name="mat_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="67883" delta="300" />
                </assert_contents>
            </output>
            <output name="mat_db_hist" file="output_23.mat.hist" />
        </test>
        <test expect_num_outputs="1">