comparison fastq_dump.xml @ 15:f5ea3ce9b9b0 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit fe3f54a0d3edb83fcf6752e3b1524c582b4febd5"

14:1790dcf3c32d

<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.3">
    <description>format from NCBI SRA</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    #if str( $outputformat ) == "fastqsanger.gz":
        --gzip
    #elif str( $outputformat ) == "fastqsanger.bz2":   
        --bzip2
    #end if
    #if $input.input_select=="file":
        --stdout
        "$input.file" > "$output_file"
    
    #elif $input.input_select=="accession_number":
        --stdout
        "\$acc" > "$output_accession" )
    #end if

    #if $input.input_select=="file_list":
        ) ; done

        ;

        for i in `ls *.fast* | cut -f 1 -d '_' | uniq` ; do

                <option value="redacted">redacted</option>
            </param>
            <param name="spotgroups" type="text" label="Filter by spot-groups" optional="true" argument="--spot-groups"/>
            <param name="clip" type="boolean" truevalue="--clip" falsevalue="" argument="--clip" label="Apply left and right clips" />
            <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads" argument="--skip-technical"/>
        </section>
    </inputs>
    <outputs>
        <collection name="list_paired" type="list:paired" label="Pair-end data (fastq-dump)">
            <filter>input['input_select'] == "file_list"</filter>

            <param name="file_list" value="list_se"/>
            <param name="maxID" value="5"/>
            <output_collection name="output_collection" type="list">
                <element name="SRR1993644" file="SRR1993644.fastqsanger"/>
            </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 fastq-dump_ utility of the SRA Toolkit.

15:f5ea3ce9b9b0

<tool id="fastq_dump" name="Download and Extract Reads in FASTA/Q" version="@VERSION@.4">
    <description>format from NCBI SRA</description>
    <macros>
        <import>sra_macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    #if str( $outputformat ) == "fastqsanger.gz":
        --gzip
    #elif str( $outputformat ) == "fastqsanger.bz2":   
        --bzip2
    #end if

    #if str($adv.table) != "":
        --table $adv.table
    #end if


    #if $input.input_select=="file":
        --stdout
        "$input.file" > "$output_file"
    
    #elif $input.input_select=="accession_number":
        --stdout
        "\$acc" > "$output_accession" )
    #end if

    #if $input.input_select=="file_list":
        "\$acc"
        ) ; done

        ;

        for i in `ls *.fast* | cut -f 1 -d '_' | uniq` ; do

                <option value="redacted">redacted</option>
            </param>
            <param name="spotgroups" type="text" label="Filter by spot-groups" optional="true" argument="--spot-groups"/>
            <param name="clip" type="boolean" truevalue="--clip" falsevalue="" argument="--clip" label="Apply left and right clips" />
            <param name="skip_technical" type="boolean" truevalue="--skip-technical" falsevalue="" checked="False" label="Dump only biological reads" argument="--skip-technical"/>
            <param name="table" label="Table name within cSRA object" type="text" value="" optional="true" help="For SRA of noisy long-reads put SEQUENCE" argument="--table"/>
        </section>
    </inputs>
    <outputs>
        <collection name="list_paired" type="list:paired" label="Pair-end data (fastq-dump)">
            <filter>input['input_select'] == "file_list"</filter>

            <param name="file_list" value="list_se"/>
            <param name="maxID" value="5"/>
            <output_collection name="output_collection" type="list">
                <element name="SRR1993644" file="SRR1993644.fastqsanger"/>
            </output_collection>
        </test>
        <test>
            <param name="input_select" value="accession_number"/>
            <param name="outputformat" value="fastqsanger.gz"/>
            <param name="accession" value="SRR6982805"/>
            <param name="maxID" value="2"/>
            <param name="table" value="SEQUENCE"/>
            <output name="output_accession" file="SRR6982805.fastqsanger.gz" ftype="fastqsanger.gz" decompress="True"/>
        </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 fastq-dump_ utility of the SRA Toolkit.