comparison fasterq_dump.xml @ 31:734abc7ac21d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 3a7f854e8ebfb2bed11198fb83181f305af633f7

30:4317d3cb6cba

                    <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
                    <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does?**

This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fasterq-dump_ utility of the SRA Toolkit.  The following applies:

31:734abc7ac21d

                    <element name="forward" file="SRR11953971_1.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
                    <element name="reverse" file="SRR11953971_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="4">
            <param name="input_select" value="file_list"/>
            <param name="file_list" value="sra_manifest.tabular" ftype="sra_manifest.tabular"/>
            <section name="adv">
                <param name="seq_defline" value="@$ac.$si/$ri $sn length=$rl"/>
            </section>
            <output_collection name="list_paired" type="list:paired" count="1">
                <element name="SRR11953971">
                    <element name="forward" ftype="fastqsanger.gz" decompress="True">
                        <assert_contents>
                            <!-- TODO replace has_size by has_line -->
                            <has_size min="56206"/>
                            <!-- <has_line line="@SRR11953971.2053/1 2053 length=101"/> -->
                        </assert_contents>
                    </element>
                    <element name="reverse" ftype="fastqsanger.gz" decompress="True">
                        <assert_contents>
                            <has_size min="59843"/>
                            <!-- <has_line line="@SRR11953971.2053/2 2053 length=101"/> -->
                        </assert_contents>
                    </element>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does?**

This tool extracts data (in fastq_ format) from the Short Read Archive (SRA) at the National Center for Biotechnology Information (NCBI). It is based on the fasterq-dump_ utility of the SRA Toolkit.  The following applies: