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comparison sra_macros.xml @ 0:9f74a22d2060 draft default tip

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sra-tools commit 70fadb7e8972b1db550d0e067584930ce1ec8673-dirty
author mvdbeek
date Wed, 04 Nov 2015 06:57:32 -0500
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-1:000000000000 0:9f74a22d2060
1 <macros>
2 <macro name="requirements">
3 <requirements>
4 <requirement type="package" version="1.1.3">ngs_sdk</requirement>
5 <requirement type="package" version="2.5.2">ncbi_vdb</requirement>
6 <requirement type="package" version="2.5.2">sra_toolkit</requirement>
7 <requirement type="package" version="3">ascp</requirement>
8 <requirement type="package" version="5.18.1">perl</requirement>
9 </requirements>
10 </macro>
11 <macro name="input_conditional">
12 <conditional name="input">
13 <param name="input_select" type="select" label="select input type">
14 <option value="accession_number">SRR accession</option>
15 <option value="file">SRA archive in current history</option>
16 </param>
17 <when value="accession_number">
18 <param name="accession" type="text" label="accession"/>
19 </when>
20 <when value="file">
21 <param format="sra" name="file" type="data" label="sra archive"/>
22 </when>
23 </conditional>
24 </macro>
25 <macro name="alignments">
26 <param name="alignments" type="select" value="both">
27 <label>aligned or unaligned reads</label>
28 <option value="both">both</option>
29 <option value="aligned">aligned only</option>
30 <option value="unaligned">unaligned only</option>
31 </param>
32 </macro>
33 <macro name="minMapq">
34 <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/>
35 </macro>
36 <macro name="region">
37 <param format="text" name="region" type="text" label="aligned region" optional="true"
38 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"/>
39 </macro>
40 <macro name="matepairDist">
41 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
42 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"/>
43 </macro>
44 <token name="@SRATOOLS_ATTRRIBUTION@">Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
45 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
46 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
47 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/mdshw5/sra-tools-galaxy.</token>
48 </macros>