comparison sra_macros.xml @ 7:c7620aa7e1f0 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
author iuc
date Wed, 10 May 2017 10:45:41 -0400
parents 26b7446bb17e
children 5e6237d58b0c
comparison
equal deleted inserted replaced
6:30775c836c77 7:c7620aa7e1f0
1 <macros> 1 <macros>
2 <token name="@VERSION@">2.8.0</token> 2 <token name="@VERSION@">2.8.1</token>
3 <macro name="requirements"> 3 <macro name="requirements">
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.8.0">sra-tools</requirement> 5 <requirement type="package" version="2.8.1">sra-tools</requirement>
6 </requirements> 6 </requirements>
7 </macro> 7 </macro>
8 <macro name="input_conditional"> 8 <macro name="input_conditional">
9 <conditional name="input"> 9 <conditional name="input">
10 <param name="input_select" type="select" label="select input type"> 10 <param name="input_select" type="select" label="select input type">
11 <option value="accession_number">SRR accession</option> 11 <option value="accession_number">SRR accession</option>
12 <option value="file_list">List of SRA accession, one per line</option>
12 <option value="file">SRA archive in current history</option> 13 <option value="file">SRA archive in current history</option>
13 <option value="file_list">List of SRA accession, one per line</option>
14 </param> 14 </param>
15 <when value="accession_number"> 15 <when value="accession_number">
16 <param name="accession" type="text" label="SRR accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 , ERR343809"/> 16 <param name="accession" type="text" label="Accession" help="Must start with SRR,DRR or ERR, e.g. SRR925743 ,ERR343809">
17 <sanitizer>
18 <valid initial="string.printable">
19 <remove value=" "/>
20 </valid>
21 <mapping initial="none">
22 <add source=" " target=""/>
23 </mapping>
24 </sanitizer>
25 </param>
17 </when> 26 </when>
18 <when value="file"> 27 <when value="file">
19 <param format="sra" name="file" type="data" label="sra archive"/> 28 <param format="sra" name="file" type="data" label="sra archive"/>
20 </when> 29 </when>
21 <when value="file_list"> 30 <when value="file_list">
22 <param format="txt" name="file_list" type="data" label="sra accession list"/> 31 <param format="txt" name="file_list" type="data" label="sra accession list"/>
23 </when> 32 </when>
24 </conditional> 33 </conditional>
25 </macro> 34 </macro>
26 <macro name="alignments"> 35 <macro name="alignments">
27 <param name="alignments" type="select" value="both"> 36 <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">
28 <label>aligned or unaligned reads</label>
29 <option value="both">both</option> 37 <option value="both">both</option>
30 <option value="aligned">aligned only</option> 38 <option value="aligned">aligned only</option>
31 <option value="unaligned">unaligned only</option> 39 <option value="unaligned">unaligned only</option>
32 </param> 40 </param>
33 </macro> 41 </macro>
34 <macro name="minMapq"> 42 <macro name="minMapq">
35 <param name="minMapq" type="integer" min="0" max="42" label="minimum mapping quality" optional="true"/> 43 <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"/>
36 </macro> 44 </macro>
37 <macro name="region"> 45 <macro name="region">
38 <param format="text" name="region" type="text" label="aligned region" optional="true" 46 <param format="text" name="region" type="text" label="aligned region" optional="true"
39 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)."/> 47 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"/>
40 </macro> 48 </macro>
41 <macro name="matepairDist"> 49 <macro name="matepairDist">
42 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true" 50 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
43 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"/> 51 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"/>
44 </macro> 52 </macro>
45 <macro name="citation"> 53 <macro name="citation">
46 <citations> 54 <citations>
47 <citation type="doi">10.1093/nar/gkq1019</citation> 55 <citation type="doi">10.1093/nar/gkq1019</citation>
48 </citations> 56 </citations>
49 </macro> 57 </macro>
58 <token name="@ACCESSION_LIST_HOWTO@">
59 -----
60
61 **How to generate accession lists**
62
63 1. Go to **SRA Run Selector** by clicking this link_
64 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*).
65 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
66 4. Click on the Runs number
67 5. On the page that would open you will see **Accession List** button
68 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.
69 </token>
70
50 <token name="@SRATOOLS_ATTRRIBUTION@"> 71 <token name="@SRATOOLS_ATTRRIBUTION@">
51 Browse the NCBI SRA for SRR accessions at http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=studies. 72 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
52 73 Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
53 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com). 74 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
54 75 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
55 Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
56
57 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
58
59 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
60
61 </token> 76 </token>
62 </macros> 77 </macros>