comparison vapor.xml @ 2:b1ca81ce88f9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 4eb29c16fda3267d50f57448a28807b03c33a96f

1:7bf891a13ace

    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">vapor</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        vapor.py
            --return_best_n $opt.return_best_n
            #if $output_type == "fasta"
                --return_seqs
            #end if
            -k '$opt.kmer_length'
            -t '$opt.score_threshold'
            -c '$opt.min_kmer_cov'
            -m '$opt.min_kmer_prop'
            -fa '$fasta_file'
            -fq '$fastq_file'
            -f '$opt.top_seed_frac'
            -q
        > out_file
    ]]>    </command>
    <inputs>

        <data name="output_fasta" from_work_dir="out_file" format="fasta" label="${tool.name} on ${on_string}: closest reference fasta">
            <filter>output_type == "fasta"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fq" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1">
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fastqsanger.gz" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1">

                <param name="score_threshold" value="0.5" />
                <param name="min_kmer_cov" value="7" />
                <param name="min_kmer_prop" value="0.5" />
                <param name="top_seed_frac" value="0.5" />
            </section>
            <output name="output_scores" file="output2.tab" />
        </test>
        <test expect_num_outputs="1">
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fq" />
            <param name="output_type" value="fasta" />
            <section name="opt">
                <param name="return_best_n" value="3" />
            </section>
            <output name="output_fasta" file="output3.fa" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

2:b1ca81ce88f9

    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">vapor</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #set $fastq_files = []
        mkdir fastq_files &&
        #for $i, $fastq in enumerate($fastq_file)
            #if $fastq.ext.endswith(".gz")
                #set $ext='.fastq.gz'
            #else
                #set $ext='.fastq'
            #end if
            #set $out = './fastq_files/input_%s%s' % ($i, $ext)
            ln -s '${fastq}' $out &&
            $fastq_files.append($out)
        #end for
        vapor.py
            --return_best_n $opt.return_best_n
            #if $output_type == "fasta"
                --return_seqs
            #end if
            -k '$opt.kmer_length'
            -t '$opt.score_threshold'
            -c '$opt.min_kmer_cov'
            -m '$opt.min_kmer_prop'
            -fa '$fasta_file'
            -fq 
            #for $fq in $fastq_files
                '${fq}'
            #end for
            -f '$opt.top_seed_frac'
            -q
        > out_file
    ]]>    </command>
    <inputs>

        <data name="output_fasta" from_work_dir="out_file" format="fasta" label="${tool.name} on ${on_string}: closest reference fasta">
            <filter>output_type == "fasta"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1"><!-- Test 1: fastq -->
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" ftype="fastq" value="test_reads.fq" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1"><!-- Test 2: multiple fastq -->
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" ftype="fastq" value="test_reads.fq,test_reads2.fq" />
            <output name="output_scores" file="output2.tab" />
        </test>
        <test expect_num_outputs="1"><!-- Test 3: fastqsanger.gz -->
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" ftype="fastqsanger.gz" value="test_reads.fastqsanger.gz" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1"><!-- Test 4: opt -->
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fastqsanger.gz" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1">

                <param name="score_threshold" value="0.5" />
                <param name="min_kmer_cov" value="7" />
                <param name="min_kmer_prop" value="0.5" />
                <param name="top_seed_frac" value="0.5" />
            </section>
            <output name="output_scores" file="output4.tab" />
        </test>
        <test expect_num_outputs="1"><!-- Test 5: fasta output-->
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fq" />
            <param name="output_type" value="fasta" />
            <section name="opt">
                <param name="return_best_n" value="3" />
            </section>
            <output name="output_fasta" file="output5.fa" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**