comparison vapor.xml @ 3:f11d2dd29b2b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit f725055ea2ccc264535ea0473bc5658de6bd3949

2:b1ca81ce88f9

<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy1" profile="21.05">
    <description>
        Classify Influenza samples from raw short read sequence data
    </description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.2</token>

    </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

            -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>
        <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" />
        <param name="fastq_file" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" multiple="true" label="FASTQ file(s)" help="WGS reads" />
        <param name="output_type" type="select" label="Output type">
            <option value="scores" selected="true">Return scores only</option>
            <option value="fasta">Return FASTA only</option>
        </param>
        <section name="opt" title="Optional arguments" expanded="true">

        <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="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fq" />
            <section name="opt">
                <param name="kmer_length" value="29" />
                <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" />

3:f11d2dd29b2b

<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy2" profile="21.05">
    <description>
        Classify Influenza samples from raw short read sequence data
    </description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.2</token>

    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">vapor</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        #if str($fastq_input.fastq_input_selector) == "paired"
            #set r1_ext = $fastq_input.fastq1.extension
            #set r2_ext = $fastq_input.fastq2.extension
            ln -s '$fastq_input.fastq1' fastq1.$r1_ext &&
            ln -s '$fastq_input.fastq2' fastq2.$r2_ext &&
        #elif str($fastq_input.fastq_input_selector) == "paired_collection"
            #set r1_ext = $fastq_input.fastq_pairs.forward.extension
            #set r2_ext = $fastq_input.fastq_pairs.reverse.extension
            ln -s '$fastq_input.fastq_pairs.forward' fastq1.$r1_ext &&
            ln -s '$fastq_input.fastq_pairs.reverse' fastq2.$r2_ext &&
        #else
            #set r1_ext = $fastq_input.fastq_single.extension
            ln -s '$fastq_input.fastq_single' fastq1.$r1_ext &&
        #end if
        vapor.py
            --return_best_n $opt.return_best_n
            #if $output_type == "fasta"
                --return_seqs
            #end if

            -t '$opt.score_threshold'
            -c '$opt.min_kmer_cov'
            -m '$opt.min_kmer_prop'
            -fa '$fasta_file'
            -fq 
            fastq1.$r1_ext
            #if str($fastq_input.fastq_input_selector) in ["paired", "paired_collection"]
                fastq2.$r2_ext
            #end if
            -f '$opt.top_seed_frac'
            -q
        > out_file
    ]]>    </command>
    <inputs>
        <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" />
        <conditional name="fastq_input">
            <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
                <option value="single">Single</option>
                <option value="paired">Paired</option>
                <option value="paired_collection">Paired Collection</option>
            </param>
            <when value="single">
                <param name="fastq_single" format="fastqsanger,fastqsanger.gz" type="data" label="FASTQ file" help="Raw short read sequences (full length reference segment sequences)" />
            </when>
            <when value="paired">
                <param name="fastq1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify reads dataset with forward reads"/>
                <param name="fastq2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify reads dataset with reverse reads"/>
            </when>
            <when value="paired_collection">
                <param name="fastq_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired" label="Select a paired collection" help="Dataset collection with forward and reverse reads"/>
            </when>
        </conditional>
        <param name="output_type" type="select" label="Output type">
            <option value="scores" selected="true">Return scores only</option>
            <option value="fasta">Return FASTA only</option>
        </param>
        <section name="opt" title="Optional arguments" expanded="true">

        <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">
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="single" />
                <param name="fastq_single" ftype="fastq" value="test_reads.fq" />
            </conditional>
            <param name="fasta_file" value="HA_sample.fa" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1">
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="paired" />
                <param name="fastq1" ftype="fastq" value="test_reads.fq" />
                <param name="fastq2" ftype="fastq" value="test_reads2.fq" />
            </conditional>
            <param name="fasta_file" value="HA_sample.fa" />
            <output name="output_scores" file="output2.tab" />
        </test>
        <test expect_num_outputs="1">
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="single" />
                <param name="fastq_single" ftype="fastqsanger.gz" value="test_reads.fastqsanger.gz" />
            </conditional>
            <param name="fasta_file" value="HA_sample.fa" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1">
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="single" />
                <param name="fastq_single" value="test_reads.fq" />
            </conditional>
            <param name="fasta_file" value="HA_sample.fa" />
            <section name="opt">
                <param name="kmer_length" value="29" />
                <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">
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="single" />
                <param name="fastq_single" value="test_reads.fq" />
            </conditional>
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="output_type" value="fasta" />
            <section name="opt">
                <param name="return_best_n" value="3" />
            </section>
            <output name="output_fasta" file="output5.fa" />