annotate sra_macros.xml @ 11:5e6237d58b0c draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2d182cef61f6cf3f732b14d2fe8dea2255271421
author iuc
date Wed, 16 May 2018 16:56:35 -0400
parents c7620aa7e1f0
children 5534eb46de20
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
1 <macros>
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
2 <token name="@VERSION@">2.8.1</token>
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
3 <macro name="requirements">
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
4 <requirements>
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
5 <requirement type="package" version="2.8.1">sra-tools</requirement>
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
6 </requirements>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
7 </macro>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
8 <macro name="input_conditional">
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
9 <conditional name="input">
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
10 <param name="input_select" type="select" label="select input type">
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
11 <option value="accession_number">SRR accession</option>
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
12 <option value="file_list">List of SRA accession, one per line</option>
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
13 <option value="file">SRA archive in current history</option>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
14 </param>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
15 <when value="accession_number">
11
5e6237d58b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2d182cef61f6cf3f732b14d2fe8dea2255271421
iuc
parents: 7
diff changeset
16 <param name="accession" type="text" label="Accession" help="Must start with SRR, DRR or ERR, e.g. SRR925743, ERR343809">
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
17 <sanitizer>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
18 <valid initial="string.printable">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
19 <remove value=" "/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
20 </valid>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
21 <mapping initial="none">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
22 <add source=" " target=""/>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
23 </mapping>
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
24 </sanitizer>
11
5e6237d58b0c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 2d182cef61f6cf3f732b14d2fe8dea2255271421
iuc
parents: 7
diff changeset
25 <validator type="empty_field" message="An accession is required"/>
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
26 </param>
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
27 </when>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
28 <when value="file">
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
29 <param format="sra" name="file" type="data" label="sra archive"/>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
30 </when>
1
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents: 0
diff changeset
31 <when value="file_list">
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents: 0
diff changeset
32 <param format="txt" name="file_list" type="data" label="sra accession list"/>
2
f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
parents: 1
diff changeset
33 </when>
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
34 </conditional>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
35 </macro>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
36 <macro name="alignments">
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
37 <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">
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
38 <option value="both">both</option>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
39 <option value="aligned">aligned only</option>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
40 <option value="unaligned">unaligned only</option>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
41 </param>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
42 </macro>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
43 <macro name="minMapq">
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
44 <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"/>
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
45 </macro>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
46 <macro name="region">
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
47 <param format="text" name="region" type="text" label="aligned region" optional="true"
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
48 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"/>
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
49 </macro>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
50 <macro name="matepairDist">
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
51 <param name="matepairDist" type="text" label="mate-pair distance (from-to|unknown)" optional="true"
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
52 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"/>
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
53 </macro>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
54 <macro name="citation">
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
55 <citations>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
56 <citation type="doi">10.1093/nar/gkq1019</citation>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
57 </citations>
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
58 </macro>
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
59 <token name="@ACCESSION_LIST_HOWTO@">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
60 -----
2
f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
parents: 1
diff changeset
61
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
62 **How to generate accession lists**
1
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents: 0
diff changeset
63
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
64 1. Go to **SRA Run Selector** by clicking this link_
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
65 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*).
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
66 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
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
67 4. Click on the Runs number
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
68 5. On the page that would open you will see **Accession List** button
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
69 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.
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
70 </token>
2
f256cb398262 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4e83a7f6d542cd3129eb14a142f74c127f91d026
iuc
parents: 1
diff changeset
71
7
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
72 <token name="@SRATOOLS_ATTRRIBUTION@">
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
73 Galaxy tool wrapper originally written by Matt Shirley (mdshw5 at gmail.com).
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
74 Wrapper modified by Philip Mabon ( philip.mabon at phac-aspc.gc.ca ).
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
75 Tool dependencies, clean-up and bug-fixes by Marius van den Beek (m.vandenbeek at gmail.com).
c7620aa7e1f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d1347141d384ed404f674d7ce408b6769e763ea1
iuc
parents: 5
diff changeset
76 For support and bug reports contact Matt Shirley or Marius van den Beek or go to https://github.com/galaxyproject/tools-iuc.
1
462ee06c9358 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit 4defaa3ff1c21e2ec39033bfe63ee69471104ede
iuc
parents: 0
diff changeset
77 </token>
0
b723c120161a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/sra-tools commit d555f296be01d0c0fa5ac28d28a48cf4ada98297
iuc
parents:
diff changeset
78 </macros>