Mercurial > repos > wolma > mimodd_ngs_run_annotation
comparison sam_header.xml @ 0:37e44e7e2d50 draft
Imported from capsule None
author | wolma |
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date | Sat, 13 Dec 2014 17:20:06 -0500 |
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-1:000000000000 | 0:37e44e7e2d50 |
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1 <tool id="ngs_run_annotation" name="NGS Run Annotation"> | |
2 <description>Create a SAM format header from run metadata for sample annotation.</description> | |
3 <requirements> | |
4 <requirement type="package" version="0.1.5">mimodd</requirement> | |
5 </requirements> | |
6 <version_command>mimodd version -q</version_command> | |
7 <command> | |
8 mimodd header | |
9 | |
10 --rg-id "$rg_id" | |
11 --rg-sm "$rg_sm" | |
12 | |
13 #if $str($rg_cn): | |
14 --rg-cn "$rg_cn" | |
15 #end if | |
16 #if $str($rg_ds): | |
17 --rg-ds "$rg_ds" | |
18 #end if | |
19 #if $str($rg_date): | |
20 --rg-dt "$rg_date" | |
21 #end if | |
22 #if $str($rg_lb): | |
23 --rg-lb "$rg_lb" | |
24 #end if | |
25 #if $str($rg_pl): | |
26 --rg-pl "$rg_pl" | |
27 #end if | |
28 #if $str($rg_pi): | |
29 --rg-pi "$rg_pi" | |
30 #end if | |
31 #if $str($rg_pu): | |
32 --rg-pu "$rg_pu" | |
33 #end if | |
34 | |
35 --ofile $outputfile | |
36 | |
37 </command> | |
38 | |
39 <inputs> | |
40 <param name="rg_id" type="text" size="80" label="read-group ID (required)"> | |
41 <sanitizer invalid_char=""> | |
42 <valid initial="string.printable"> | |
43 <remove value=""" /> | |
44 </valid> | |
45 <mapping initial="none"> | |
46 <add source=""" target="\""/> | |
47 </mapping> | |
48 </sanitizer> | |
49 </param> | |
50 <param name="rg_sm" type="text" size="80" label="sample name (required)"> | |
51 <sanitizer invalid_char=""> | |
52 <valid initial="string.printable"> | |
53 <remove value=""" /> | |
54 </valid> | |
55 <mapping initial="none"> | |
56 <add source=""" target="\""/> | |
57 </mapping> | |
58 </sanitizer> | |
59 </param> | |
60 <param name="rg_ds" type="text" size="80" label="description"> | |
61 <sanitizer invalid_char=""> | |
62 <valid initial="string.printable"> | |
63 <remove value=""" /> | |
64 </valid> | |
65 <mapping initial="none"> | |
66 <add source=""" target="\""/> | |
67 </mapping> | |
68 </sanitizer> | |
69 </param> | |
70 <param name="rg_date" type="text" label="date (YYYY-MM-DD) the run was produced" /> | |
71 <param name="rg_cn" type="text" size="80" label="name of sequencing center"> | |
72 <sanitizer invalid_char=""> | |
73 <valid initial="string.printable"> | |
74 <remove value=""" /> | |
75 </valid> | |
76 <mapping initial="none"> | |
77 <add source=""" target="\""/> | |
78 </mapping> | |
79 </sanitizer> | |
80 </param> | |
81 <param name="rg_lb" type="text" size="80" label="read-group library"> | |
82 <sanitizer invalid_char=""> | |
83 <valid initial="string.printable"> | |
84 <remove value=""" /> | |
85 </valid> | |
86 <mapping initial="none"> | |
87 <add source=""" target="\""/> | |
88 </mapping> | |
89 </sanitizer> | |
90 </param> | |
91 <param name="rg_pl" type="text" label="platform/technology used to produce the reads" /> | |
92 <param name="rg_pi" type="text" label="predicted median insert size" /> | |
93 <param name="rg_pu" type="text" size="80" label="platform unit; unique identifier"> | |
94 <sanitizer invalid_char=""> | |
95 <valid initial="string.printable"> | |
96 <remove value=""" /> | |
97 </valid> | |
98 <mapping initial="none"> | |
99 <add source=""" target="\""/> | |
100 </mapping> | |
101 </sanitizer> | |
102 </param> | |
103 </inputs> | |
104 | |
105 <outputs> | |
106 <data name="outputfile" format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/> | |
107 </outputs> | |
108 | |
109 <help> | |
110 .. class:: infomark | |
111 | |
112 **What it does** | |
113 | |
114 This tool takes the user-provided information about a next-generation sequencing run and constructs a valid header in the SAM file format from it. | |
115 | |
116 The result file can be used by the tools *Convert* and *Reheader* or in the *SNAP Read Alignment* step to add run metadata to sequenced reads files (or to overwrite pre-existing information). | |
117 | |
118 **Note:** | |
119 | |
120 **MiModD requires run metadata for every input file at the Alignment step !** | |
121 | |
122 **Tip:** | |
123 | |
124 While you can do Alignments from fastq file format by providing a custom header file directly to the *SNAP Read Alignment* tool, we **recommend** you to first convert all input files to and archive all datasets in SAM/BAM format with appropriate header information prior to any downstream analysis. Although a bit more time-consuming, this practice protects against information loss and ensures that the input datasets will remain useful for others in the future. | |
125 | |
126 </help> | |
127 </tool> | |
128 |