annotate sam_header.xml @ 20:aba6d9b1c1f1 draft

Uploaded
author wolma
date Fri, 29 Apr 2016 06:01:46 -0400
parents 93db2f9bca12
children c46406466625
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
93db2f9bca12 upgrade to v0.1.7.2
Wolfgang Maier wolfgang.maier@biologie.uni-freiburg.de
parents: 8
diff changeset
1 <tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.2">
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
2 <description>Create a SAM format header from run metadata for sample annotation.</description>
2
72d20758ba2c final upload
wolma
parents: 1
diff changeset
3 <macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
4 <import>toolshed_macros.xml</import>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
5 </macros>
72d20758ba2c final upload
wolma
parents: 1
diff changeset
6 <expand macro="requirements"/>
0
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
7 <version_command>mimodd version -q</version_command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
8 <command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
9 mimodd header
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
10
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
11 --rg-id "$rg_id"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
12 --rg-sm "$rg_sm"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
13
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
14 #if $str($rg_cn):
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
15 --rg-cn "$rg_cn"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
16 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
17 #if $str($rg_ds):
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
18 --rg-ds "$rg_ds"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
19 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
20 #if $str($rg_date):
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
21 --rg-dt "$rg_date"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
22 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
23 #if $str($rg_lb):
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
24 --rg-lb "$rg_lb"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
25 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
26 #if $str($rg_pl):
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
27 --rg-pl "$rg_pl"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
28 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
29 #if $str($rg_pi):
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
30 --rg-pi "$rg_pi"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
31 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
32 #if $str($rg_pu):
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
33 --rg-pu "$rg_pu"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
34 #end if
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
35
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
36 --ofile "$outputfile"
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
37
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
38 </command>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
39
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
40 <inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
41 <param name="rg_id" type="text" size="80" label="read-group ID (required)">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
42 <sanitizer invalid_char="">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
43 <valid initial="string.printable">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
44 <remove value="&quot;" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
45 </valid>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
46 <mapping initial="none">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
47 <add source="&quot;" target="\&quot;"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
48 </mapping>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
49 </sanitizer>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
50 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
51 <param name="rg_sm" type="text" size="80" label="sample name (required)">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
52 <sanitizer invalid_char="">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
53 <valid initial="string.printable">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
54 <remove value="&quot;" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
55 </valid>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
56 <mapping initial="none">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
57 <add source="&quot;" target="\&quot;"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
58 </mapping>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
59 </sanitizer>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
60 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
61 <param name="rg_ds" type="text" size="80" label="description">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
62 <sanitizer invalid_char="">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
63 <valid initial="string.printable">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
64 <remove value="&quot;" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
65 </valid>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
66 <mapping initial="none">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
67 <add source="&quot;" target="\&quot;"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
68 </mapping>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
69 </sanitizer>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
70 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
71 <param name="rg_date" type="text" label="date (YYYY-MM-DD) the run was produced" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
72 <param name="rg_cn" type="text" size="80" label="name of sequencing center">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
73 <sanitizer invalid_char="">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
74 <valid initial="string.printable">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
75 <remove value="&quot;" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
76 </valid>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
77 <mapping initial="none">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
78 <add source="&quot;" target="\&quot;"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
79 </mapping>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
80 </sanitizer>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
81 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
82 <param name="rg_lb" type="text" size="80" label="read-group library">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
83 <sanitizer invalid_char="">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
84 <valid initial="string.printable">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
85 <remove value="&quot;" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
86 </valid>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
87 <mapping initial="none">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
88 <add source="&quot;" target="\&quot;"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
89 </mapping>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
90 </sanitizer>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
91 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
92 <param name="rg_pl" type="text" label="platform/technology used to produce the reads" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
93 <param name="rg_pi" type="text" label="predicted median insert size" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
94 <param name="rg_pu" type="text" size="80" label="platform unit; unique identifier">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
95 <sanitizer invalid_char="">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
96 <valid initial="string.printable">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
97 <remove value="&quot;" />
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
98 </valid>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
99 <mapping initial="none">
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
100 <add source="&quot;" target="\&quot;"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
101 </mapping>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
102 </sanitizer>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
103 </param>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
104 </inputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
105
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
106 <outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
107 <data name="outputfile" format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
108 </outputs>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
109
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
110 <help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
111 .. class:: infomark
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
112
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
113 **What it does**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
114
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
115 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
116
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
117 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).
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
118
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
119 **Note:**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
120
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
121 **MiModD requires run metadata for every input file at the Alignment step !**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
122
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
123 **Tip:**
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
124
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
125 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.
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
126
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
127 </help>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
128 </tool>
6231ae8f87b8 Uploaded
wolma
parents:
diff changeset
129