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comparison sam_header.xml @ 0:aa82b2e54055 draft

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planemo upload for repository https://github.com/wm75/mimodd_galaxy_wrappers commit b36048cd608ede0ec6f6559648525c9350caae34-dirty
author wolma
date Sat, 11 Nov 2017 18:19:22 -0500
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children 1425ea794026
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-1:000000000000 0:aa82b2e54055
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 <sanitizer invalid_char="">
45 <valid initial="string.printable">
46 <remove value="&quot;" />
47 </valid>
48 <mapping initial="none">
49 <add source="&quot;" target="\&quot;"/>
50 </mapping>
51 </sanitizer>
52 </param>
53 <param name="rg_sm" type="text" size="80"
54 label="sample name (required)">
55 <validator type="empty_field" />
56 <sanitizer invalid_char="">
57 <valid initial="string.printable">
58 <remove value="&quot;" />
59 </valid>
60 <mapping initial="none">
61 <add source="&quot;" target="\&quot;"/>
62 </mapping>
63 </sanitizer>
64 </param>
65 <param name="rg_ds" type="text" size="80" label="description">
66 <sanitizer invalid_char="">
67 <valid initial="string.printable">
68 <remove value="&quot;" />
69 </valid>
70 <mapping initial="none">
71 <add source="&quot;" target="\&quot;"/>
72 </mapping>
73 </sanitizer>
74 </param>
75 <param name="rg_date" type="text"
76 label="date (YYYY-MM-DD) the run was produced">
77 <validator type="expression" message="YYYY-MM-DD date format required">not value or (len(value.split('-')) == 3 and all(part.isdigit() and len(part)==expect_len for part, expect_len in zip(value.split('-'), [4,2,2])))</validator>
78 </param>
79 <param name="rg_cn" type="text" size="80"
80 label="name of sequencing center">
81 <sanitizer invalid_char="">
82 <valid initial="string.printable">
83 <remove value="&quot;" />
84 </valid>
85 <mapping initial="none">
86 <add source="&quot;" target="\&quot;"/>
87 </mapping>
88 </sanitizer>
89 </param>
90 <param name="rg_lb" type="text" size="80" label="read-group library">
91 <sanitizer invalid_char="">
92 <valid initial="string.printable">
93 <remove value="&quot;" />
94 </valid>
95 <mapping initial="none">
96 <add source="&quot;" target="\&quot;"/>
97 </mapping>
98 </sanitizer>
99 </param>
100 <param name="rg_pl" type="text"
101 label="platform/technology used to produce the reads">
102 <option value="ILLUMINA">ILLUMINA</option>
103 <option value="PACBIO">PACBIO</option>
104 <option value="IONTORRENT">IONTORRENT</option>
105 <option value="ONT">ONT</option>
106 <option value="LS454">LS454</option>
107 <option value="SOLID">SOLID</option>
108 <option value="HELICOS">HELICOS</option>
109 <option value="CAPILLARY">CAPILLARY</option>
110 </param>
111 <param name="rg_pi" type="text" label="predicted median insert size" />
112 <param name="rg_pu" type="text" size="80"
113 label="platform unit; unique identifier">
114 <sanitizer invalid_char="">
115 <valid initial="string.printable">
116 <remove value="&quot;" />
117 </valid>
118 <mapping initial="none">
119 <add source="&quot;" target="\&quot;"/>
120 </mapping>
121 </sanitizer>
122 </param>
123 </inputs>
124
125 <outputs>
126 <data name="ofile" format="sam"
127 label="${rg_sm} (${rg_id}) header information from MiModd ${tool.name} on ${on_string}"/>
128 </outputs>
129
130 <tests>
131 <test>
132 <param name="rg_id" value="000" />
133 <param name="rg_sm" value="N2" />
134 <param name="rg_ds" value="C. elegans wt" />
135 <param name="rg_date" value="2017-06-27" />
136 <param name="rg_cn" value="ABC" />
137 <param name="rg_lb" value="XYZ" />
138 <param name="rg_pl" value="ILLUMINA" />
139 <param name="rg_pi" value="400" />
140 <param name="rg_pu" value="SEQ123" />
141 <output name="ofile" ftype="sam" file="header_only.sam" />
142 </test>
143 </tests>
144
145 <help><![CDATA[
146 .. class:: infomark
147
148 **What it does**
149
150 This tool takes user-provided information about a next-generation sequencing
151 run and constructs a valid SAM format header from it.
152
153 The resulting dataset can be used by the *MiModD Convert*, *MiModD Reheader*
154 and the *MiModD Read Alignment* tool to add run metadata to sequenced reads
155 input datasets (or to overwrite pre-existing information).
156
157 **Note:**
158
159 **MiModD requires run metadata for every input file at the Alignment step !**
160
161 **Tip:**
162
163 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.
164
165 @HELP_FOOTER@
166 ]]></help>
167 <expand macro="citations" />
168 </tool>
169