comparison stacks_kmerfilter.xml @ 3:1544278c272e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit 9a6c14bcb90c0b30c583294a993fac47504f4009"

2:8a55d29c8fcf

        </section>-->
        <expand macro="in_log"/>
    </inputs>
    <outputs>
        <expand macro="out_log"/>
        <expand macro="fastq_output_filter">
            <filter>not options_kmer_char['k_dist'] and not options_kmer_char['write_k_freq']</filter>
        </expand>
        <data format="tabular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies">
            <filter>options_kmer_char['k_dist']</filter>
        </data>

                <has_text text="--abundant"/>
                <has_text text="--k_len 16"/>
            </assert_command>
            <param name="add_log" value="yes"/>
            <output name="output_log"><assert_contents><has_text text="5 retained reads."/></assert_contents></output>
            <output name="clean" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Removed1_0001.1.1.fq.single.gz"/>
        </test>
        <test expect_num_outputs="7">
            <conditional name="input_type">
                <param name="input_type_select" value="paired"/>
                <param name="fqinputs">

                <has_text text="--normalize 1"/>
            </assert_command>
            <param name="add_log" value="yes"/>
            <output name="output_log"><assert_contents><has_text text="8 retained reads."/></assert_contents></output>
            <output_collection name="clean_pair" type="paired">
                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Removed1_0001.1.1.fq.gz"/>
                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Removed2_0001.2.2.fq.gz"/>
            </output_collection>
            <output_collection name="discarded_pair" type="paired">
                <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Discarded1_0001.1.1.fq.gz"/>
                <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Discarded2_0001.2.2.fq.gz"/>
            </output_collection>
        </test>
        <!-- kfreq output -->
        <test expect_num_outputs="2">
            <conditional name="input_type">

3:1544278c272e

        </section>-->
        <expand macro="in_log"/>
    </inputs>
    <outputs>
        <expand macro="out_log"/>
        <expand macro="fastq_output_filter" format="fastq">
            <filter>not options_kmer_char['k_dist'] and not options_kmer_char['write_k_freq']</filter>
        </expand>
        <data format="tabular" name="kfreq" label="${tool.name} on ${on_string} kmer frequencies">
            <filter>options_kmer_char['k_dist']</filter>
        </data>

                <has_text text="--abundant"/>
                <has_text text="--k_len 16"/>
            </assert_command>
            <param name="add_log" value="yes"/>
            <output name="output_log"><assert_contents><has_text text="5 retained reads."/></assert_contents></output>
            <output name="clean" compare="diff" ftype="fastq" file="kmerfilter/Removed1_0001.1.1.fq.single"/>
        </test>
        <test expect_num_outputs="7">
            <conditional name="input_type">
                <param name="input_type_select" value="paired"/>
                <param name="fqinputs">

                <has_text text="--normalize 1"/>
            </assert_command>
            <param name="add_log" value="yes"/>
            <output name="output_log"><assert_contents><has_text text="8 retained reads."/></assert_contents></output>
            <output_collection name="clean_pair" type="paired">
                <element name="forward" compare="diff" ftype="fastq" file="kmerfilter/Removed1_0001.1.1.fq"/>
                <element name="reverse" compare="diff" ftype="fastq" file="kmerfilter/Removed2_0001.2.2.fq"/>
            </output_collection>
            <output_collection name="discarded_pair" type="paired">
                <element name="forward" compare="diff" ftype="fastq" file="kmerfilter/Discarded1_0001.1.1.fq"/>
                <element name="reverse" compare="diff" ftype="fastq" file="kmerfilter/Discarded2_0001.2.2.fq"/>
            </output_collection>
        </test>
        <!-- kfreq output -->
        <test expect_num_outputs="2">
            <conditional name="input_type">