comparison pysradb.xml @ 1:f63cf0adfd87 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pysradb commit ce41250f1a9525090296ce9351b8a38a521af6b1

0:1005ffbccd86

                help="Sequence Read Archive (SRA) data, is the largest publicly available repository of high throughput sequencing data. The European Nucleotide 
                    Archive (ENA) provides a comprehensive record of nucleotide sequencing information.">
                <option value="sra">SRA: Sequence Read Archive</option>
                <option value="ena">ENA: European Nucleotide Archive</option>
            </param>
            <param argument="--query" type="text" value=""
                label="Query keywords" help="Multiple keywords should be separated by spaces. Example: colorectal cancer">
                <sanitizer invalid_char="">
                    <valid initial="string.letters,string.digits">
                        <add value="_" />
                        <add value="-" />
                        <add value=" " />
                    </valid>
                </sanitizer>
                <validator type="regex">[0-9a-zA-Z_ -]+</validator>
            </param>
            <conditional name="conditional_mode">
                <param name="selector" type="select" label="Genetic material recovered directly from environmental or clinical samples" help="Enable this option if you are interested in metagenomic data. Default: disabled">
                    <option value="false" selected="true">Disabled</option>
                    <option value="true">Enabled</option>
                </param>
                <when value="false">
                    <expand macro="source_macro">

                </output_collection>
            </test>
            <!-- Test 02: Specific search options-->
            <test expect_num_outputs="2">
                <param name="database" value="sra"/>
                <param name="query" value="colorectal cancer"/>
                <conditional name="conditional_platform">
                    <param name="platform" value="illumina"/>
                    <param name="instrument" value="NovaSeq 6000"/>
                </conditional>
                <param name="strategy" value="wga"/>

                    <param name="max" value="50"/>
                </section>
                <conditional name="conditional_mode">
                    <param name="selector" value="false"/>
                    <param name="source" value="genomic"/>
                    <param name="organism" value="homo sapiens"/>
                </conditional>
                <output name="metadata_file" file="test_03.tabular" ftype="tsv"/>
                <output name="stats" file="test_03.txt" ftype="txt"/>
            </test>
            <!-- Test 04: Test metatranscriptome query -->

1:f63cf0adfd87

                help="Sequence Read Archive (SRA) data, is the largest publicly available repository of high throughput sequencing data. The European Nucleotide 
                    Archive (ENA) provides a comprehensive record of nucleotide sequencing information.">
                <option value="sra">SRA: Sequence Read Archive</option>
                <option value="ena">ENA: European Nucleotide Archive</option>
            </param>
            <param argument="--query" type="text" value="" optional="true"
                label="Query keywords/BioProject ID" help="Multiple keywords should be separated by spaces. Example: colorectal cancer">
                <sanitizer invalid_char="">
                    <valid initial="string.letters,string.digits">
                        <add value="_" />
                        <add value="-" />
                        <add value=" " />
                    </valid>
                </sanitizer>
                <validator type="regex">[0-9a-zA-Z_ -]+</validator>
            </param>
            <conditional name="conditional_mode">
                <param name="selector" type="select" label="Metagenomic data" help="Enable this option if you are interested in genetic material recovered directly from environmental or clinical samples. Default: disabled">
                    <option value="false" selected="true">Disabled</option>
                    <option value="true">Enabled</option>
                </param>
                <when value="false">
                    <expand macro="source_macro">

                </output_collection>
            </test>
            <!-- Test 02: Specific search options-->
            <test expect_num_outputs="2">
                <param name="database" value="sra"/>
                <conditional name="conditional_platform">
                    <param name="platform" value="illumina"/>
                    <param name="instrument" value="NovaSeq 6000"/>
                </conditional>
                <param name="strategy" value="wga"/>

                    <param name="max" value="50"/>
                </section>
                <conditional name="conditional_mode">
                    <param name="selector" value="false"/>
                    <param name="source" value="genomic"/>
                    <param name="organism" value="Homo sapiens"/>
                </conditional>
                <output name="metadata_file" file="test_03.tabular" ftype="tsv"/>
                <output name="stats" file="test_03.txt" ftype="txt"/>
            </test>
            <!-- Test 04: Test metatranscriptome query -->