comparison ncbi_acc_download.xml @ 2:e063168e0a81 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_acc_download commit 7077bbc8c1e416f717b545c5ac18b0c8b5a066b2

1:28587613264f

        ncbi-acc-download
            --molecule '${molecule.select}'
            --format '${molecule.format}'
            #if $molecule.format != 'featuretable' and $molecule.format != 'gff3':
                --extended-validation all
            #end if
            \${accession};
        failure=\$?;
        if [ \$failure -ne 0 ]; then
            echo " failed." >> ../error.log;

                <param name="format" type="select" label="File Format">
                    <option value="fasta" selected="true">FASTA</option>
                </param>
            </when>
        </conditional>
        <param name="ignore_failed" type="select" display="radio"
        label="How to handle download failures">
            <option value="0">Abort with error on first failure</option>
            <option value="1">Add accession to failed list and continue</option>
        </param>

                        <has_line line=">NP_003192.1 transcription factor A, mitochondrial isoform 1 precursor [Homo sapiens]" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does**
Given a file containing a list of NCBI accession numbers or a direct entry of accession numbers in the tool text input box, this tool will download the corresponding sequence records via the NCBI API. 

2:e063168e0a81

        ncbi-acc-download
            --molecule '${molecule.select}'
            --format '${molecule.format}'
            #if $molecule.format != 'featuretable' and $molecule.format != 'gff3':
                --extended-validation all
            #end if
            #if $range != ""
                --range $range
            #end if
            \${accession};
        failure=\$?;
        if [ \$failure -ne 0 ]; then
            echo " failed." >> ../error.log;

                <param name="format" type="select" label="File Format">
                    <option value="fasta" selected="true">FASTA</option>
                </param>
            </when>
        </conditional>
        <param argument="--range" type="text" label="Range" help="Region to subset accession. Start and end position separated by ':', '..', or '.'. Only for single accession">
            <sanitizer invalid_char="">
                <valid initial="string.digits">
                    <add value=":" />
                    <add value=".." />
                    <add value="." />
                </valid>
            </sanitizer>
        </param>
        <param name="ignore_failed" type="select" display="radio"
        label="How to handle download failures">
            <option value="0">Abort with error on first failure</option>
            <option value="1">Add accession to failed list and continue</option>
        </param>

                        <has_line line=">NP_003192.1 transcription factor A, mitochondrial isoform 1 precursor [Homo sapiens]" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
        <test>
            <conditional name="molecule">
                <param name="select" value="nucleotide"/>
                <param name="format" value="genbank"/>
            </conditional>
            <conditional name="query_source">
                <param name="select" value="accession_list" />
                <param name="accession_list" value="NC_006666"/>
            </conditional>
            <param name="range" value="1697:2764"/>
            <output_collection name="output" type="list">
                <element name="NC_006666" ftype="genbank">
                    <assert_contents>
                        <has_text text="ND2" />
                        <not_has_text text="tRNA-Ile" />
                    </assert_contents>
                </element>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
**What it does**
Given a file containing a list of NCBI accession numbers or a direct entry of accession numbers in the tool text input box, this tool will download the corresponding sequence records via the NCBI API.