<macros>
    <token name="@VERSION@">2.8.1</token>
    <macro name="requirements">
        <requirements>
            <requirement type="package" version="2.8.1">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>
                </param>
            </when>
            <when value="file">
                <param format="sra" name="file" type="data" label="sra archive"/>
            </when>
            <when value="file_list">
                <param format="txt" name="file_list" type="data" label="sra accession list"/>
            </when>
        </conditional>
    </macro>
    <macro name="alignments">
        <param name="alignments" type="select" value="both" label="Output aligned or unaligned reads" help="Output reads according to their alignment status." argument="--aligned and --unaligned">
            <option value="both">both</option>
            <option value="aligned">aligned only</option>
            <option value="unaligned">unaligned only</option>
        </param>
    </macro>
    <macro name="minMapq">
        <param name="minMapq" type="integer" min="0" max="42" label="Minimum mapping quality" optional="true" help="Minimum mapping quality an alignment has to have, to be dumped." argument="--min-mapq"/>
    </macro>
    <macro name="region">
        <param format="text" name="region" type="text" label="aligned region" optional="true"
               help="Filter by position on genome. Can be either accession.version (ex: NC_000001.10), chromosome name (ex:chr1 or 1) or 1-based coordinates (ex: chr1:1-101)." argument="--aligned-region"/>
    </macro>
    <macro name="matepairDist">
        <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
               help="Filter by distance between matepairs. Use unknown to find matepairs split between the references. Use from-to (inclusive) to limit matepair distance on the same reference" argument="--matepair-distance"/>
    </macro>
    <macro name="citation">
        <citations>
            <citation type="doi">10.1093/nar/gkq1019</citation>
        </citations>
    </macro>
    <token name="@ACCESSION_LIST_HOWTO@">
-----

**How to generate accession lists**

 1. Go to **SRA Run Selector** by clicking this link_
 2. Find the study you are interested in by typing a search term within the **Search** box. This can be a word (e.g., *mitochondria*) or an accession you have gotten from a paper (e.g., *SRR1582967*). 
 3. Once you click on the study of interest you will see the number of datasets in this study within the **Related SRA data** box
 4. Click on the Runs number
 5. On the page that would open you will see **Accession List** button
 6. Clicking of this button will produce a file that you will need to upload into Galaxy and use as the input to this tool.
    </token>

    <token name="@SRATOOLS_ATTRRIBUTION@">
Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
    </token>
</macros>