comparison fastq_dump.xml @ 32:fb723c531be5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit ac10fe34f1b2d5e8109dcaaf42b7870bee57827b

31:734abc7ac21d

    <command detect_errors="exit_code"><![CDATA[
    @COPY_CONFIGFILE@
    @SET_ACCESSIONS@

    #if $input.input_select == "sra_file":
        fastq-dump --log-level fatal --accession '${input.file.name}'
    #else:
        ## Do not use prefetch if region is specified, to avoid downloading
        ## the complete sra file.
        #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
            prefetch -X 200000000 "\$acc" &&
        #end if
        fastq-dump --accession "\$acc"
        --split-files
    #end if
    --defline-seq '$adv.defline_seq'
    --defline-qual '+'

    $adv.split
    #if str( $adv.alignments ) == "aligned":

                        </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:

32:fb723c531be5

    <command detect_errors="exit_code"><![CDATA[
    @COPY_CONFIGFILE@
    @SET_ACCESSIONS@

    #if $input.input_select == "sra_file":
        fastq-dump --log-level fatal --accession "\$acc"
    #else:
        ## Do not use prefetch if region is specified, to avoid downloading
        ## the complete sra file.
        #if ( str( $adv.region ) == "" ) and ( str( $adv.minID ) == "" ) and ( str( $adv.maxID ) == "" ):
            prefetch -X 200000000 "\$acc" &&
        #end if
        fastq-dump --accession "\$acc"
    #end if
    --split-files
    --defline-seq '$adv.defline_seq'
    --defline-qual '+'

    $adv.split
    #if str( $adv.alignments ) == "aligned":

                        </assert_contents>
                    </element>
                </element>
            </output_collection>
        </test>
        <test expect_num_outputs="2">
            <param name="input_select" value="sra_file"/>
            <param name="sra_file" value="SRR522874.sra"/>
            <param name="split" value="True"/>
            <param name="skip_technical" value="True"/>
            <section name="adv">
                <param name="defline_seq" value="@$sn/$ri"/>
            </section>
            <output_collection name="list_paired" type="list:paired" count="1">
                <element name="SRR522874.sra">
                    <element name="forward" file="SRR522874.sra_2.fastq.gz" ftype="fastqsanger.gz" decompress="True"/>
                    <element name="reverse" file="SRR522874.sra_4.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: