comparison mitohifi.xml @ 1:99ddbf037d98 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mitohifi commit 59301409d1f555702e346d7b6ba3992a4f336691

0:f6065bc6e428

            --email '${operation_mode.email}'
            --outfolder ./ 
            #if $operation_mode.min_length
                --min_length $operation_mode.min_length
            #end if
            $operation_mode.exact_specie
            && mv ./*fasta ./reference_genome.fasta
            && mv ./*gb ./reference_genome.gb
        #elif $operation_mode.command == 'mitohifi'
            ln -s '${operation_mode.reference_genbank}' related_mito.gb
            && ln -s '${operation_mode.reference_fasta}' related_mito.fasta

            && mitohifi_v2.py 
            #if $operation_mode.input_option.input == 'pacbio'
                -r '${ ' '.join(["%s" % $x for $x in $operation_mode.input_option.input_reads]) }'
                -m $operation_mode.input_option.bloom_filter
            #else
                -c '${operation_mode.input_option.input_assembly}'

            <param name="command" type="select" label="Operation type selector" help="Select a type of operation">
                <option value="find_reference">Find a close-related mitochondrial reference genome</option>
                <option value="mitohifi">Run MitoHiFi</option>
            </param>
            <when value="find_reference">
                <param argument="--species" type="text" value="" label="Specie name" help="Specie name in binomial nomenclature">
                    <sanitizer invalid_char="">
                        <valid initial="string.letters,string.digits">
                            <add value=" "/>
                        </valid>
                    </sanitizer>

                        </valid>
                    </sanitizer>
                </param>
                <param argument="--min_length" type="integer" 
                    min="0" max="15000000" value="" optional="True" label="Minimal appropriate length" />
                <param name="exact_specie" argument="-s" type="boolean" 
                    truevalue="-s" falsevalue="" checked="False" optional="True" label="Search for an exact species"/>
            </when>
            <when value="mitohifi">
                <conditional name="input_option">
                    <param name="input" type="select" label="Input mode">

            <filter> operation_mode['command'] == 'mitohifi'</filter>
        </data>
        <data name="mitogenome_genbank" format="genbank" from_work_dir="final_mitogenome.gb" label="${tool.name} on ${on_string}: final mitogenome (genbank)">
            <filter> operation_mode['command'] == 'mitohifi'</filter>
        </data>
        <data name="parsed_blast" format="txt" from_work_dir="contigs_filtering/parsed_blast.txt" label="${tool.name} on ${on_string}: parsed BLAST">
            <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter>
        </data> 
        <data name="parsed_blast_all" format="txt" from_work_dir="contigs_filtering/parsed_blast_all.txt" label="${tool.name} on ${on_string}: parsed BLAST (all)">
            <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter>

                <param name="email" value="[e-mail]"/>
                <param name="min_length" value="1500"/>
            </conditional>
            <output name="fasta_reference" ftype="fasta">
                <assert_contents>
                    <has_size value="15742"/>
                    <has_line line=">NC_054179.1 Spodoptera exempta mitochondrion, complete genome"/>
                </assert_contents>
            </output>
            <output name="genbank_reference" ftype="genbank">
                <assert_contents>
                    <has_size value="43468"/>
                    <has_line line="DEFINITION  Spodoptera exempta mitochondrion, complete genome."/>
                </assert_contents>
            </output>
        </test>
        <!--Test 02-->
        <test expect_num_outputs="5">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz"/>

                <assert_contents>
                    <has_size value="15329"/>
                    <has_line line=">ptg000001c"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 03-->
        <test expect_num_outputs="5">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line=">ptg000001c"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 04-->
        <test expect_num_outputs="5">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line=">ptg000001c"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 05-->
        <test expect_num_outputs="5">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name='input' value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line=">ptg000001c"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 06-->
        <test expect_num_outputs="8">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name='input' value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line="ptg000001c"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 07-->
        <test expect_num_outputs="6">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_size value="28"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 08-->
        <test expect_num_outputs="6">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name='input' value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line="DEFINITION  NC_016067.1_rc_rotated"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 10-->
        <test expect_num_outputs="6">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

1:99ddbf037d98

            --email '${operation_mode.email}'
            --outfolder ./ 
            #if $operation_mode.min_length
                --min_length $operation_mode.min_length
            #end if
            $operation_mode.exact_species
            && mv ./*fasta ./reference_genome.fasta
            && mv ./*gb ./reference_genome.gb
        #elif $operation_mode.command == 'mitohifi'
            ln -s '${operation_mode.reference_genbank}' related_mito.gb
            && ln -s '${operation_mode.reference_fasta}' related_mito.fasta

            && mitohifi.py 
            #if $operation_mode.input_option.input == 'pacbio'
                -r '${ ' '.join(["%s" % $x for $x in $operation_mode.input_option.input_reads]) }'
                -m $operation_mode.input_option.bloom_filter
            #else
                -c '${operation_mode.input_option.input_assembly}'

            <param name="command" type="select" label="Operation type selector" help="Select a type of operation">
                <option value="find_reference">Find a close-related mitochondrial reference genome</option>
                <option value="mitohifi">Run MitoHiFi</option>
            </param>
            <when value="find_reference">
                <param argument="--species" type="text" value="" label="Species name" help="Species name in binomial nomenclature">
                    <sanitizer invalid_char="">
                        <valid initial="string.letters,string.digits">
                            <add value=" "/>
                        </valid>
                    </sanitizer>

                        </valid>
                    </sanitizer>
                </param>
                <param argument="--min_length" type="integer" 
                    min="0" max="15000000" value="" optional="True" label="Minimal appropriate length" />
                <param name="exact_species" argument="-s" type="boolean" 
                    truevalue="-s" falsevalue="" checked="False" optional="True" label="Search for an exact species"/>
            </when>
            <when value="mitohifi">
                <conditional name="input_option">
                    <param name="input" type="select" label="Input mode">

            <filter> operation_mode['command'] == 'mitohifi'</filter>
        </data>
        <data name="mitogenome_genbank" format="genbank" from_work_dir="final_mitogenome.gb" label="${tool.name} on ${on_string}: final mitogenome (genbank)">
            <filter> operation_mode['command'] == 'mitohifi'</filter>
        </data>
        <data name="mitogenome_annotation" format="png" from_work_dir="final_mitogenome.annotation.png" label="${tool.name} on ${on_string}: final mitogenome annotation (png)">
            <filter> operation_mode['command'] == 'mitohifi'</filter>
        </data>
        <data name="mitogenome_coverage" format="png" from_work_dir="final_mitogenome.coverage.png" label="${tool.name} on ${on_string}: final mitogenome coverage (png)">
            <filter> operation_mode['command'] == 'mitohifi'</filter>
        </data>
        <data name="contigs_stats" format="tsv" from_work_dir="contigs_stats.tsv" label="${tool.name} on ${on_string}: contigs stats (TSV)">
            <filter> operation_mode['command'] == 'mitohifi'</filter>
        </data>
        <data name="parsed_blast" format="txt" from_work_dir="contigs_filtering/parsed_blast.txt" label="${tool.name} on ${on_string}: parsed BLAST">
            <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter>
        </data> 
        <data name="parsed_blast_all" format="txt" from_work_dir="contigs_filtering/parsed_blast_all.txt" label="${tool.name} on ${on_string}: parsed BLAST (all)">
            <filter>operation_mode['command'] == 'mitohifi' and (operation_mode['advanced_options']['outputs'] and 'contigs_filtering' in operation_mode['advanced_options']['outputs'])</filter>

                <param name="email" value="[e-mail]"/>
                <param name="min_length" value="1500"/>
            </conditional>
            <output name="fasta_reference" ftype="fasta">
                <assert_contents>
                    <has_size value="15593"/>
                    <has_line line=">NC_062101.1 Condica capensis mitochondrion, complete genome"/>
                </assert_contents>
            </output>
            <output name="genbank_reference" ftype="genbank">
                <assert_contents>
                    <has_size value="43220"/>
                    <has_line line="DEFINITION  Condica capensis mitochondrion, complete genome."/>
                </assert_contents>
            </output>
        </test>
        <!--Test 02-->
        <!--<test expect_num_outputs="8">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz"/>

                <assert_contents>
                    <has_size value="15329"/>
                    <has_line line=">ptg000001c"/>
                </assert_contents>
            </output>
        </test>-->
        <!--Test 03-->
        <test expect_num_outputs="8">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line=">ptg000001c"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 04-->
        <test expect_num_outputs="8">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line=">ptg000001c"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 05-->
        <test expect_num_outputs="8">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name='input' value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line=">ptg000001c"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 06-->
        <test expect_num_outputs="11">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name='input' value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line="ptg000001c"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 07-->
        <test expect_num_outputs="9">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_size value="28"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 08-->
        <test expect_num_outputs="9">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name='input' value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>

                    <has_line line="DEFINITION  NC_016067.1_rc_rotated"/>
                </assert_contents>
            </output>
        </test>
        <!--Test 10-->
        <test expect_num_outputs="9">
            <conditional name="operation_mode">
                <param name="command" value="mitohifi"/>
                <conditional name="input_option">
                    <param name="input" value="pacbio"/>
                    <param name="input_reads" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>