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comparison sam_header.xml @ 23:5db0545b9004 draft

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update to v0.1.7.3
author wolma
date Thu, 21 Jul 2016 03:55:49 -0400
parents c46406466625
children
comparison
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22:24154c580718 23:5db0545b9004
1 <tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.2"> 1 <tool id="ngs_run_annotation" name="NGS Run Annotation" version="0.1.7.3">
2 <description>Create a SAM format header from run metadata for sample annotation.</description> 2 <description>Create a SAM format header from run metadata for sample annotation.</description>
3 <macros> 3 <macros>
4 <import>toolshed_macros.xml</import> 4 <import>toolshed_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements" />
7 <version_command>python3 -m MiModD version -q</version_command> 7 <version_command>python3 -m MiModD version -q</version_command>
8 <command> 8 <command>
9 python3 -m MiModD header 9 python3 -m MiModD header
10 10
11 --rg-id "$rg_id" 11 --rg-id "$rg_id"
36 --ofile "$outputfile" 36 --ofile "$outputfile"
37 37
38 </command> 38 </command>
39 39
40 <inputs> 40 <inputs>
41 <param name="rg_id" type="text" size="80" label="read-group ID (required)"> 41 <param label="read-group ID (required)" name="rg_id" size="80" type="text">
42 <sanitizer invalid_char=""> 42 <sanitizer invalid_char="">
43 <valid initial="string.printable"> 43 <valid initial="string.printable">
44 <remove value="&quot;" /> 44 <remove value="&quot;" />
45 </valid> 45 </valid>
46 <mapping initial="none"> 46 <mapping initial="none">
47 <add source="&quot;" target="\&quot;"/> 47 <add source="&quot;" target="\&quot;" />
48 </mapping> 48 </mapping>
49 </sanitizer> 49 </sanitizer>
50 </param> 50 </param>
51 <param name="rg_sm" type="text" size="80" label="sample name (required)"> 51 <param label="sample name (required)" name="rg_sm" size="80" type="text">
52 <sanitizer invalid_char=""> 52 <sanitizer invalid_char="">
53 <valid initial="string.printable"> 53 <valid initial="string.printable">
54 <remove value="&quot;" /> 54 <remove value="&quot;" />
55 </valid> 55 </valid>
56 <mapping initial="none"> 56 <mapping initial="none">
57 <add source="&quot;" target="\&quot;"/> 57 <add source="&quot;" target="\&quot;" />
58 </mapping> 58 </mapping>
59 </sanitizer> 59 </sanitizer>
60 </param> 60 </param>
61 <param name="rg_ds" type="text" size="80" label="description"> 61 <param label="description" name="rg_ds" size="80" type="text">
62 <sanitizer invalid_char=""> 62 <sanitizer invalid_char="">
63 <valid initial="string.printable"> 63 <valid initial="string.printable">
64 <remove value="&quot;" /> 64 <remove value="&quot;" />
65 </valid> 65 </valid>
66 <mapping initial="none"> 66 <mapping initial="none">
67 <add source="&quot;" target="\&quot;"/> 67 <add source="&quot;" target="\&quot;" />
68 </mapping> 68 </mapping>
69 </sanitizer> 69 </sanitizer>
70 </param> 70 </param>
71 <param name="rg_date" type="text" label="date (YYYY-MM-DD) the run was produced" /> 71 <param label="date (YYYY-MM-DD) the run was produced" name="rg_date" type="text" />
72 <param name="rg_cn" type="text" size="80" label="name of sequencing center"> 72 <param label="name of sequencing center" name="rg_cn" size="80" type="text">
73 <sanitizer invalid_char=""> 73 <sanitizer invalid_char="">
74 <valid initial="string.printable"> 74 <valid initial="string.printable">
75 <remove value="&quot;" /> 75 <remove value="&quot;" />
76 </valid> 76 </valid>
77 <mapping initial="none"> 77 <mapping initial="none">
78 <add source="&quot;" target="\&quot;"/> 78 <add source="&quot;" target="\&quot;" />
79 </mapping> 79 </mapping>
80 </sanitizer> 80 </sanitizer>
81 </param> 81 </param>
82 <param name="rg_lb" type="text" size="80" label="read-group library"> 82 <param label="read-group library" name="rg_lb" size="80" type="text">
83 <sanitizer invalid_char=""> 83 <sanitizer invalid_char="">
84 <valid initial="string.printable"> 84 <valid initial="string.printable">
85 <remove value="&quot;" /> 85 <remove value="&quot;" />
86 </valid> 86 </valid>
87 <mapping initial="none"> 87 <mapping initial="none">
88 <add source="&quot;" target="\&quot;"/> 88 <add source="&quot;" target="\&quot;" />
89 </mapping> 89 </mapping>
90 </sanitizer> 90 </sanitizer>
91 </param> 91 </param>
92 <param name="rg_pl" type="text" label="platform/technology used to produce the reads" /> 92 <param label="platform/technology used to produce the reads" name="rg_pl" type="text" />
93 <param name="rg_pi" type="text" label="predicted median insert size" /> 93 <param label="predicted median insert size" name="rg_pi" type="text" />
94 <param name="rg_pu" type="text" size="80" label="platform unit; unique identifier"> 94 <param label="platform unit; unique identifier" name="rg_pu" size="80" type="text">
95 <sanitizer invalid_char=""> 95 <sanitizer invalid_char="">
96 <valid initial="string.printable"> 96 <valid initial="string.printable">
97 <remove value="&quot;" /> 97 <remove value="&quot;" />
98 </valid> 98 </valid>
99 <mapping initial="none"> 99 <mapping initial="none">
100 <add source="&quot;" target="\&quot;"/> 100 <add source="&quot;" target="\&quot;" />
101 </mapping> 101 </mapping>
102 </sanitizer> 102 </sanitizer>
103 </param> 103 </param>
104 </inputs> 104 </inputs>
105 105
106 <outputs> 106 <outputs>
107 <data name="outputfile" format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/> 107 <data format="sam" label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}" name="outputfile" />
108 </outputs> 108 </outputs>
109 109
110 <help> 110 <help>
111 .. class:: infomark 111 .. class:: infomark
112 112
124 124
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. 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.
126 126
127 </help> 127 </help>
128 </tool> 128 </tool>
129