comparison novoplasty.xml @ 3:15200570e926 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/novoplasty commit a53d7313e06ca38b6bf24a58c72a8dfd702de862"

2:64a1c751d99b

<?xml version="1.0"?>
<tool id="novoplasty" name="NOVOplasty" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
    <description>de novo assembler for short circular genomes</description>
    <macros>
        <token name="@TOOL_VERSION@">4.2</token>
        <token name="@VERSION_SUFFIX@">1</token>
        <xml name="content" token_min="" token_max="">
            <param name="genome_range_min" type="text" value="@MIN@" label="Set lower limit for the expected genome size range" help="(Genome Range)"/>
            <param name="genome_range_max" type="text" value="@MAX@" label="Set upper limit for the expected genome size range" help="(Genome Range)"/>
        </xml>
    </macros>

Max memory            = 
Extended log          = 1
Save assembled reads  = ${optional.save_assembled_reads}
Seed Input            = ${seed_input}
Extend seed directly  = ${assembly_options.extend_seed_directly}
Reference sequence    = #if $reference_cond.use_reference == 'true' and $reference_cond.reference then $reference_cond.reference else ''#
Variance detection    = #if $reference_cond.use_reference == 'true' then $reference_cond.variance_detection else ''#
Chloroplast sequence  = #if $assembly_options.type_cond.type_sel == 'mito_plant' and $assembly_options.type_cond.chloroplast_sequence then $assembly_options.type_cond.chloroplast_sequence else ''#

Dataset 1:
-----------------------
Read Length           = ${read_options.read_length}
Insert size           = ${read_options.insert_size}
Platform              = ${read_options.platform}
Single/Paired         = PE
Combined reads        = #if $reads_cond.reads_sel == 'combined' then 'combined.'+$reads_cond.combined_reads.datatype.file_ext else ''#
Forward reads         = #if $reads_cond.reads_sel == 'separate' then 'forward.'+$reads_cond.forward_reads.datatype.file_ext else ''#
Reverse reads         = #if $reads_cond.reads_sel == 'separate' then 'reverse.'+$reads_cond.reverse_reads.datatype.file_ext else ''#

Heteroplasmy:
-----------------------
MAF                   = #if $reference_cond.use_reference == 'true' and $reference_cond.heteroplasmy_cond.detect_heteroplasmy == 'true' then $reference_cond.heteroplasmy_cond.maf else ''#
HP exclude list       = ## option not available
PCR-free              = #if $reference_cond.use_reference == 'true' and $reference_cond.heteroplasmy_cond.detect_heteroplasmy == 'true' then $reference_cond.heteroplasmy_cond.pcr_free else ''#

Optional:
-----------------------
Insert size auto      = ${optional.insert_size_auto}
Insert Range          = ${optional.insert_range}
Insert Range strict   = ${optional.insert_range_strict}
Use Quality Scores    = ${optional.use_quality_scores}
        ]]></configfile>
    </configfiles>
    <inputs>
        <!-- Currently only PE reads is supported

            <param name="extend_seed_directly" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Extend seeds instead of finding matching reads" help="Only use this when your seed originates from the same sample and there are no possible mismatches. (Extend seed directly)"/>
            <param name="kmer" type="integer" value="39" min="1" label="Set length of overlap between matching reads" help="If reads are shorter then 90 bp or you have low coverage data, this value should be decreased down to 23. For reads longer then 101 bp, this value can be increased, but this is not necessary. (kmer)"/>
        </section>
        <section name="optional" title="Optional options">
            <param name="insert_size_auto" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Finetune your insert size automatically?" help="(Insert size auto)"/>
            <param name="insert_range" type="float" min="0" value="1.6" label="Insert range" help="This variation on the insert size, could lower it when the coverage is very high or raise it when the coverage is too low [use default in the first run]." />
            <param name="insert_range_strict" type="float" min="0" value="1.2" label="Insert range strict" help="Strict variation to resolve repetitive regions [use default in the first run]." />    
            <param name="use_quality_scores" type="boolean" truevalue="yes" falsevalue="no" label="Take quality scores into account?" help="Only use this when reads have low quality, like with the 300 bp reads of Illumina. (Use Quality Scores)"/>
            <param name="save_assembled_reads" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Retain original IDs when saving assemled reads?" help="All the reads used for the assembly will be stored in seperate files. (Save assembled reads)"/>
        </section>
        <param name="out" type="select" multiple="true" optional="true" display="checkboxes" label="Additional output files">
            <option value="config">Config file</option>

                    <has_text_matching expression=".+Assembly 1 finished.+"/>
                </assert_contents>
            </output>
            <output name="out_config">
                <assert_contents>
                    <has_n_lines n="39"/>
                    <has_line line="Project:"/>
                    <has_text_matching expression=".+"/>
                </assert_contents>
            </output>
        </test>

                </assert_contents>
            </output>
            <!-- Variance -->
            <output name="out_v">
                <assert_contents>
                    <has_n_lines n="21"/>
                    <has_line line="##fileformat=VCFv4.0"/>
                    <has_text_matching expression="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
                </assert_contents>
            </output>
            <!-- Others -->

                    <has_text_matching expression=".+Assembly 1 finished.+"/>
                </assert_contents>
            </output>
            <output name="out_config">
                <assert_contents>
                    <has_n_lines n="39"/>
                    <has_line line="Project:"/>
                    <has_text_matching expression=".+"/>
                </assert_contents>
            </output>
        </test>

                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- #9 Test insert range options -->
        <test expect_num_outputs="6">
            <conditional name="reads_cond">
                <param name="reads_sel" value="separate"/>
                    <param name="forward_reads" value="forward.fasta.gz"/>
                    <param name="reverse_reads" value="reverse.fasta.gz"/>
            </conditional>
            <section name="assembly_options">
                <conditional name="type_cond">
                    <param name="type_sel" value="mito"/>
                </conditional>
            </section>
            <section name="optional">
                <param name="insert_range" value="1.9"/>
                <param name="insert_range_strict" value="1.3"/>
            </section>    
            <!-- fasta.gz not supported -->
            <param name="seed_input" value="seed.fasta"/>
            <!-- Assembly -->
            <output name="out_c">
                <assert_contents>
                    <has_n_lines n="110"/>
                </assert_contents>
            </output>
            <output name="out_ct">
                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>
            <output name="out_ua">
                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- #10 Test save assembled reads option -->
        <test expect_num_outputs="8">
            <conditional name="reads_cond">
                <param name="reads_sel" value="separate"/>
                    <param name="forward_reads" value="forward.fasta.gz"/>

3:15200570e926

<tool id="novoplasty" name="NOVOplasty" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="18.01">
    <description>de novo assembler for short circular genomes</description>
    <macros>
        <token name="@TOOL_VERSION@">4.3.1</token>
        <token name="@VERSION_SUFFIX@">0</token>
        <xml name="content" token_min="" token_max="">
            <param name="genome_range_min" type="text" value="@MIN@" label="Set lower limit for the expected genome size range" help="(Genome Range)"/>
            <param name="genome_range_max" type="text" value="@MAX@" label="Set upper limit for the expected genome size range" help="(Genome Range)"/>
        </xml>
    </macros>

Max memory            = 
Extended log          = 1
Save assembled reads  = ${optional.save_assembled_reads}
Seed Input            = ${seed_input}
Extend seed directly  = ${assembly_options.extend_seed_directly}
Reference sequence    = #if $reference_cond.use_reference == 'true' and $reference_cond.reference then $reference_cond.reference else ''
Variance detection    = #if $reference_cond.use_reference == 'true' then $reference_cond.variance_detection else ''
Chloroplast sequence  = #if $assembly_options.type_cond.type_sel == 'mito_plant' and $assembly_options.type_cond.chloroplast_sequence then $assembly_options.type_cond.chloroplast_sequence else ''


Dataset 1:
-----------------------
Read Length           = ${read_options.read_length}
Insert size           = ${read_options.insert_size}
Platform              = ${read_options.platform}
Single/Paired         = PE
Combined reads        = #if $reads_cond.reads_sel == 'combined' then 'combined.'+$reads_cond.combined_reads.datatype.file_ext else ''
Forward reads         = #if $reads_cond.reads_sel == 'separate' then 'forward.'+$reads_cond.forward_reads.datatype.file_ext else ''
Reverse reads         = #if $reads_cond.reads_sel == 'separate' then 'reverse.'+$reads_cond.reverse_reads.datatype.file_ext else ''

Heteroplasmy:
-----------------------
MAF                   = #if $reference_cond.use_reference == 'true' and $reference_cond.heteroplasmy_cond.detect_heteroplasmy == 'true' then $reference_cond.heteroplasmy_cond.maf else ''
HP exclude list       = ## option not available
PCR-free              = #if $reference_cond.use_reference == 'true' and $reference_cond.heteroplasmy_cond.detect_heteroplasmy == 'true' then $reference_cond.heteroplasmy_cond.pcr_free else ''

Optional:
-----------------------
Insert size auto      = ${optional.insert_size_auto}
Use Quality Scores    = ${optional.use_quality_scores}
        ]]></configfile>
    </configfiles>
    <inputs>
        <!-- Currently only PE reads is supported

            <param name="extend_seed_directly" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Extend seeds instead of finding matching reads" help="Only use this when your seed originates from the same sample and there are no possible mismatches. (Extend seed directly)"/>
            <param name="kmer" type="integer" value="39" min="1" label="Set length of overlap between matching reads" help="If reads are shorter then 90 bp or you have low coverage data, this value should be decreased down to 23. For reads longer then 101 bp, this value can be increased, but this is not necessary. (kmer)"/>
        </section>
        <section name="optional" title="Optional options">
            <param name="insert_size_auto" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Finetune your insert size automatically?" help="(Insert size auto)"/>
            <param name="use_quality_scores" type="boolean" truevalue="yes" falsevalue="no" label="Take quality scores into account?" help="Only use this when reads have low quality, like with the 300 bp reads of Illumina. (Use Quality Scores)"/>
            <param name="save_assembled_reads" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Retain original IDs when saving assemled reads?" help="All the reads used for the assembly will be stored in seperate files. (Save assembled reads)"/>
        </section>
        <param name="out" type="select" multiple="true" optional="true" display="checkboxes" label="Additional output files">
            <option value="config">Config file</option>

                    <has_text_matching expression=".+Assembly 1 finished.+"/>
                </assert_contents>
            </output>
            <output name="out_config">
                <assert_contents>
                    <has_n_lines n="38"/>
                    <has_line line="Project:"/>
                    <has_text_matching expression=".+"/>
                </assert_contents>
            </output>
        </test>

                </assert_contents>
            </output>
            <!-- Variance -->
            <output name="out_v">
                <assert_contents>
                    <has_n_lines n="20"/>
                    <has_line line="##fileformat=VCFv4.0"/>
                    <has_text_matching expression="#CHROM&#009;POS&#009;ID&#009;REF&#009;ALT&#009;QUAL&#009;FILTER&#009;INFO"/>
                </assert_contents>
            </output>
            <!-- Others -->

                    <has_text_matching expression=".+Assembly 1 finished.+"/>
                </assert_contents>
            </output>
            <output name="out_config">
                <assert_contents>
                    <has_n_lines n="38"/>
                    <has_line line="Project:"/>
                    <has_text_matching expression=".+"/>
                </assert_contents>
            </output>
        </test>

                <assert_contents>
                    <has_n_lines n="0"/>
                </assert_contents>
            </output>
        </test>
        <!-- #9 Test insert range options 
        Test removed because those options are not available -->

        <!-- #10 Test save assembled reads option -->
        <test expect_num_outputs="8">
            <conditional name="reads_cond">
                <param name="reads_sel" value="separate"/>
                    <param name="forward_reads" value="forward.fasta.gz"/>