comparison sra_macros.xml @ 13:c38286ea7047 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 686710a7d313b828f1daed20c4055479727f2d91

12:5534eb46de20

<macros>
    <token name="@VERSION@">2.9.1</token>
    <macro name="requirements">
        <requirements>
            <requirement type="package" version="2.9.1">sra-tools</requirement>
        </requirements>
    </macro>
    <macro name="input_conditional">
        <conditional name="input">
            <param name="input_select" type="select" label="select input type">
                <option value="accession_number">SRR accession</option>
                <option value="file_list">List of SRA accession, one per line</option>
                <option value="file">SRA archive in current history</option>
            </param>
            <when value="accession_number">
                <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
                    <sanitizer>
                        <valid initial="string.printable">
                            <remove value=" "/>
                        </valid>
                        <mapping initial="none">
                            <add source=" " target=""/>
                        </mapping>
                    </sanitizer>
                    <validator type="empty_field" message="An accession is required"/>
                </param>
            </when>
            <when value="file">
                <param format="sra" name="file" type="data" label="sra archive"/>

13:c38286ea7047

<macros>
    <token name="@VERSION@">2.9.1</token>
    <token name="@ACCESSIONS_FROM_FILE@">
        grep '^[[:space:]]*[E|S|D]RR[0-9]\{1,\}[[:space:]]*$'
    </token>
    <token name="@SET_ACCESSIONS@"><![CDATA[
        #if $input.input_select=="file_list":
            for acc in `@ACCESSIONS_FROM_FILE@ '$input.file_list'` ;
            do (
        #elif $input.input_select=="accession_number":
            acc='${input.accession}' && [ ""\$acc" =~ ^[E|S|D]RR[0-9]{1,}$" ] && (
        #end if
    ]]></token>

    <macro name="requirements">
        <requirements>
            <requirement type="package" version="2.9.1">sra-tools</requirement>
        </requirements>
    </macro>
    <macro name="sanitize_query">
        <sanitizer>
            <valid initial="string.printable">
                <remove value=" "/>
                <remove value="&apos;" />
            </valid>
            <mapping initial="none">
                <add source=" " target=""/>
                <add source="&apos;" target="&apos;&quot;&apos;&quot;&apos;" />
            </mapping>
        </sanitizer>
    </macro>
    <macro name="input_conditional">
        <conditional name="input">
            <param name="input_select" type="select" label="select input type">
                <option value="accession_number">SRR accession</option>
                <option value="file_list">List of SRA accession, one per line</option>
                <option value="file">SRA archive in current history</option>
            </param>
            <when value="accession_number">
                <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
                    <expand macro="sanitize_query" />
                    <validator type="empty_field" message="An accession is required"/>
                </param>
            </when>
            <when value="file">
                <param format="sra" name="file" type="data" label="sra archive"/>