Mercurial > repos > mvdbeek > sra_tools
comparison sra_macros.xml @ 0:68527898a9ea draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 92d32947393757598262fbaed175b2c6fd84c181
| author | mvdbeek |
|---|---|
| date | Fri, 25 Sep 2015 09:28:56 -0400 |
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| -1:000000000000 | 0:68527898a9ea |
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| 1 <macros> | |
| 2 <macro name="requirements"> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.5.2">sra_toolkit</requirement> | |
| 5 <requirement type="package" version="3">ascp</requirement> | |
| 6 <requirement type="package" version="5.18.1">perl</requirement> | |
| 7 </requirements> | |
| 8 </macro> | |
| 9 <macro name="input_conditional"> | |
| 10 <conditional name="input"> | |
| 11 <param name="input_select" type="select" label="select input type"> | |
| 12 <option value="accession_number">SRR accession</option> | |
| 13 <option value="file">SRA archive in current history</option> | |
| 14 </param> | |
| 15 <when value="accession_number"> | |
| 16 <param name="accession" type="text" label="accession"/> | |
| 17 </when> | |
| 18 <when value="file"> | |
| 19 <param format="sra" name="file" type="data" label="sra archive"/> | |
| 20 </when> | |
| 21 </conditional> | |
| 22 </macro> | |
| 23 <macro name="alignments"> | |
| 24 <param name="alignments" type="select" value="both"> | |
| 25 <label>aligned or unaligned reads</label> | |
| 26 <option value="both">both</option> | |
| 27 <option value="aligned">aligned only</option> | |
| 28 <option value="unaligned">unaligned only</option> | |
| 29 </param> | |
| 30 </macro> | |
| 31 <macro name="minMapq"> | |
| 32 <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/> | |
| 33 </macro> | |
| 34 <macro name="region"> | |
| 35 <param format="text" name="region" type="text" label="aligned region" optional="true" | |
| 36 help="Filter by position on genome. Name can either be accession.version (ex: NC_000001.10) or file specific name (ex:chr1 or 1). from and to are 1-based coordinates"/> | |
| 37 </macro> | |
| 38 <macro name="matepairDist"> | |
| 39 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" | |
| 40 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"/> | |
| 41 </macro> | |
| 42 <token name="@SRATOOLS_ATTRRIBUTION@">Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. | |
| 43 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com). | |
| 44 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com). | |
| 45 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/mdshw5/sra-tools-galaxy.</token> | |
| 46 </macros> |