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comparison sam_header.xml @ 0:f0f2795de2c7 draft

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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit 528bcf3b769c7c73f119b2a176d19071f9ef5312
author wolma
date Tue, 19 Dec 2017 04:54:04 -0500
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-1:000000000000 0:f0f2795de2c7
1 <tool id="mimodd_header" name="MiModD Run Annotation" version="@MIMODD_WRAPPER_VERSION@">
2 <description>
3 writes run metadata in SAM format for attaching it to sequenced reads data
4 </description>
5 <macros>
6 <import>macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="stdio" />
10 <expand macro="version_command" />
11 <command><![CDATA[
12 mimodd header
13 --rg-id '$rg_id'
14 --rg-sm '$rg_sm'
15 #if $str($rg_cn):
16 --rg-cn '$rg_cn'
17 #end if
18 #if $str($rg_ds):
19 --rg-ds '$rg_ds'
20 #end if
21 #if $str($rg_date):
22 --rg-dt '$rg_date'
23 #end if
24 #if $str($rg_lb):
25 --rg-lb '$rg_lb'
26 #end if
27 #if $str($rg_pl):
28 --rg-pl '$rg_pl'
29 #end if
30 #if $str($rg_pi):
31 --rg-pi '$rg_pi'
32 #end if
33 #if $str($rg_pu):
34 --rg-pu '$rg_pu'
35 #end if
36 --ofile '$ofile'
37
38 ]]></command>
39
40 <inputs>
41 <param name="rg_id" type="text" size="80"
42 label="read-group ID (required)">
43 <validator type="empty_field" />
44 <expand macro="lex_sam_header" />
45 </param>
46 <param name="rg_sm" type="text" size="80"
47 label="sample name (required)">
48 <validator type="empty_field" />
49 <expand macro="lex_sam_header" />
50 </param>
51 <param name="rg_ds" type="text" size="80" label="description">
52 <expand macro="lex_sam_header" />
53 </param>
54 <param name="rg_date" type="text"
55 label="date (YYYY-MM-DD) the run was produced">
56 <expand macro="YYYY-MM-DD_format_validator" />
57 </param>
58 <param name="rg_cn" type="text" size="80"
59 label="name of sequencing center">
60 <expand macro="lex_sam_header" />
61 </param>
62 <param name="rg_lb" type="text" size="80" label="read-group library">
63 <expand macro="lex_sam_header" />
64 </param>
65 <param name="rg_pl" type="text"
66 label="platform/technology used to produce the reads">
67 <expand macro="known_sequencing_platform options" />
68 <expand macro="lex_sam_header" />
69 </param>
70 <param name="rg_pi" type="text" label="predicted median insert size">
71 <validator type="expression" message="an integer number is required">not value or value.isdigit()</validator>
72 </param>
73 <param name="rg_pu" type="text" size="80"
74 label="platform unit; unique identifier">
75 <expand macro="lex_sam_header" />
76 </param>
77 </inputs>
78
79 <outputs>
80 <data name="ofile" format="sam"
81 label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/>
82 </outputs>
83
84 <tests>
85 <test>
86 <param name="rg_id" value="000" />
87 <param name="rg_sm" value="N2" />
88 <param name="rg_ds" value="C. elegans wt" />
89 <param name="rg_date" value="2017-06-27" />
90 <param name="rg_cn" value="ABC" />
91 <param name="rg_lb" value="XYZ" />
92 <param name="rg_pl" value="ILLUMINA" />
93 <param name="rg_pi" value="400" />
94 <param name="rg_pu" value="SEQ123" />
95 <output name="ofile" ftype="sam" file="header_only.sam" />
96 </test>
97 </tests>
98
99 <help><![CDATA[
100 .. class:: infomark
101
102 **What it does**
103
104 This tool takes user-provided information about a next-generation sequencing
105 run and constructs a valid SAM format header from it.
106
107 The resulting dataset can be used by the *MiModD Convert*, *MiModD Reheader*
108 and the *MiModD Read Alignment* tool to add run metadata to sequenced reads
109 input datasets (or to overwrite pre-existing information).
110
111 **Note:**
112
113 **MiModD requires run metadata for every input file at the Alignment step !**
114
115 **Tip:**
116
117 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.
118
119 @HELP_FOOTER@
120 ]]></help>
121 <expand macro="citations" />
122 </tool>
123