comparison vsnp_statistics.xml @ 5:d0fbdeaaa488 draft

"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_statistics commit 770e89322a15829580ed9577a853660f63233f32"

4:2d6c6b01319e

    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.16.5">numpy</requirement>
        <requirement type="package" version="0.25.3">pandas</requirement>
        <requirement type="package" version="1.2.0">xlrd</requirement>
        <requirement type="package" version="1.2.8">xlsxwriter</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#import re
#set input_idxstats_dir = 'input_idxstats'
#set input_metrics_dir = 'input_metrics'

                <param name="vsnp_azc" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP: add zero coverage metrics files"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="xlsx"/>
    </outputs>
    <tests>
        <!-- A single fastq file -->
        <test expect_num_outputs="1">
            <param name="input_type" value="single_files"/>
            <param name="read_type" value="single"/>
            <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/>
            <param name="vsnp_azc" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/>
            <output name="output" file="vsnp_statistics1.xlsx" ftype="xlsx" compare="sim_size"/>
        </test>
        <!-- A set of paired fastq files -->
        <test expect_num_outputs="1">
            <param name="input_type" value="single_files"/>
            <param name="read_type" value="pair"/>
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/>
            <param name="vsnp_azc" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/>
            <output name="output" file="vsnp_statistics2.xlsx" ftype="xlsx" compare="sim_size"/>
        </test>
        <!-- A collection of SE fastq files -->
        <test expect_num_outputs="1">
            <param name="input_type" value="collections"/>
            <param name="read_type" value="single"/>

                <collection type="list">
                    <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="add_zc_metrics3.tabular" dbkey="89"/>
                    <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="add_zc_metrics4.tabular" dbkey="89"/>
                </collection>
            </param>
            <output name="output" file="vsnp_statistics3.xlsx" ftype="xlsx" compare="sim_size"/>
        </test>
        <!-- A collection of PE fastq files -->
        <test expect_num_outputs="1">
            <param name="input_type" value="collections"/>
            <param name="collection_type" value="paired"/>

            <param name="vsnp_azc">
                <collection type="list">
                    <element name="13-1941-6_S4_L001_R1_600000.fastq" value="add_zc_metrics5.tabular" dbkey="89"/>
                </collection>
            </param>
            <output name="output" file="vsnp_statistics4.xlsx" ftype="xlsx" compare="sim_size"/>
        </test>
    </tests>
    <help>
**What it does**

5:d0fbdeaaa488

    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.78">biopython</requirement>
        <requirement type="package" version="1.16.5">numpy</requirement>
        <requirement type="package" version="0.25.3">pandas</requirement>
        <requirement type="package" version="1.2.0">xlrd</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#import re
#set input_idxstats_dir = 'input_idxstats'
#set input_metrics_dir = 'input_metrics'

                <param name="vsnp_azc" type="data_collection" format="tabular" collection_type="list" label="Collection of vSNP: add zero coverage metrics files"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="tabular"/>
    </outputs>
    <tests>
        <!-- A single fastq file -->
        <test expect_num_outputs="1">
            <param name="input_type" value="single_files"/>
            <param name="read_type" value="single"/>
            <param name="read1" value="Mcap_Deer_DE_SRR650221.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="samtools_idxstats" value="samtools_idxstats1.tabular" ftype="tabular" dbkey="89"/>
            <param name="vsnp_azc" value="add_zc_metrics1.tabular" ftype="tabular" dbkey="89"/>
            <output name="output" file="vsnp_statistics1.tabular" ftype="tabular"/>
        </test>
        <!-- A set of paired fastq files -->
        <test expect_num_outputs="1">
            <param name="input_type" value="single_files"/>
            <param name="read_type" value="pair"/>
            <param name="read1" value="13-1941-6_S4_L001_R1_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="read2" value="13-1941-6_S4_L001_R2_600000.fastq.gz" ftype="fastqsanger.gz" dbkey="89"/>
            <param name="samtools_idxstats" value="samtools_idxstats2.tabular" ftype="tabular" dbkey="89"/>
            <param name="vsnp_azc" value="add_zc_metrics2.tabular" ftype="tabular" dbkey="89"/>
            <output name="output" file="vsnp_statistics2.tabular" ftype="tabular"/>
        </test>
        <!-- A collection of SE fastq files -->
        <test expect_num_outputs="1">
            <param name="input_type" value="collections"/>
            <param name="read_type" value="single"/>

                <collection type="list">
                    <element name="13-1941-6_S4_L001_R1_600000.fastq.gz" value="add_zc_metrics3.tabular" dbkey="89"/>
                    <element name="Mcap_Deer_DE_SRR650221.fastq.gz" value="add_zc_metrics4.tabular" dbkey="89"/>
                </collection>
            </param>
            <output name="output" file="vsnp_statistics3.tabular" ftype="tabular"/>
        </test>
        <!-- A collection of PE fastq files -->
        <test expect_num_outputs="1">
            <param name="input_type" value="collections"/>
            <param name="collection_type" value="paired"/>

            <param name="vsnp_azc">
                <collection type="list">
                    <element name="13-1941-6_S4_L001_R1_600000.fastq" value="add_zc_metrics5.tabular" dbkey="89"/>
                </collection>
            </param>
            <output name="output" file="vsnp_statistics4.tabular" ftype="tabular"/>
        </test>
    </tests>
    <help>
**What it does**