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comparison sra_macros.xml @ 0:20da3b075bbf draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
author iuc
date Sun, 06 Dec 2015 09:00:59 -0500
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-1:000000000000 0:20da3b075bbf
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="5.18.1">perl</requirement>
8 </requirements>
9 </macro>
10 <macro name="input_conditional">
11 <conditional name="input">
12 <param name="input_select" type="select" label="select input type">
13 <option value="accession_number">SRR accession</option>
14 <option value="file">SRA archive in current history</option>
15 </param>
16 <when value="accession_number">
17 <param name="accession" type="text" label="SRR accession" help="Must start with SRR, e.g. SRR925743"/>
18 </when>
19 <when value="file">
20 <param format="sra" name="file" type="data" label="sra archive"/>
21 </when>
22 </conditional>
23 </macro>
24 <macro name="alignments">
25 <param name="alignments" type="select" value="both">
26 <label>aligned or unaligned reads</label>
27 <option value="both">both</option>
28 <option value="aligned">aligned only</option>
29 <option value="unaligned">unaligned only</option>
30 </param>
31 </macro>
32 <macro name="minMapq">
33 <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/>
34 </macro>
35 <macro name="region">
36 <param format="text" name="region" type="text" label="aligned region" optional="true"
37 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)."/>
38 </macro>
39 <macro name="matepairDist">
40 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
41 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"/>
42 </macro>
43 <macro name="citation">
44 <citations>
45 <citation type="doi">10.1093/nar/gkq1019</citation>
46 </citations>
47 </macro>
48 <token name="@SRATOOLS_ATTRRIBUTION@">Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies.
49 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
50 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
51 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.</token>
52 </macros>