comparison fastq_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="2">
            <param name="input_select" value="accession_number"/>
            <param name="outputformat" value="fastqsanger.gz"/>
            <param name="accession" value="ERR086330, SRR11953971"/>
            <section name="adv">
                <param name="defline_seq" value="@$ac.$si/$ri $sn length=$rl"/>
            </section>
            <output_collection name="list_paired" type="list:paired" count="2">
                <element name="ERR086330">
                    <element name="forward" ftype="fastqsanger.gz" decompress="True">
                        <assert_contents>
                            <!-- decompressed content assertions only work from 23.1
                                 therefore we test for size being at least one byte
                                 larger than the results of the previous test which
                                 uses the shorter default deflines
                                 TODO replace has_size by has_line-->
                            <has_size min="147"/>
                            <!-- <has_line line="@ERR086330.1/1 1 length=76"/> -->
                        </assert_contents>
                    </element>
                    <element name="reverse" ftype="fastqsanger.gz" decompress="True">
                        <assert_contents>
                            <has_size min="141"/>
                            <!-- <has_line line="@ERR086330.1/2 1 length=76"/> -->
                        </assert_contents>
                    </element>
                </element>
                <element name="SRR11953971">
                    <element name="forward" ftype="fastqsanger.gz" decompress="True">
                        <assert_contents>
                            <has_size min="56206"/>
                            <!-- <has_line line="@SRR11953971.1/1 1 length=101"/> -->
                        </assert_contents>
                    </element>
                    <element name="reverse" ftype="fastqsanger.gz" decompress="True">
                        <assert_contents>
                            <has_size min="59843"/>
                            <!-- <has_line line="@SRR11953971.1/2 1 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: