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comparison bwa_macros.xml @ 5:fbf460831036 draft

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planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
author devteam
date Tue, 21 Jul 2015 13:51:02 -0400
parents ac30bfd3e2a8
children 09a7281d24c5
comparison
equal deleted inserted replaced
4:ac30bfd3e2a8 5:fbf460831036
1 <macros> 1 <macros>
2 2 <import>read_group_macros.xml</import>
3 <token name="@set_rg_string@"> 3 <token name="@set_rg_string@">
4 #set $rg_string = "@RG\tID:" + str($rg.ID) + "\tSM:" + str($rg.SM) + "\tPL:" + str($rg.PL) 4 #set $rg_string = "@RG\tID:" + str($rg_id)
5 #if $rg.LB 5 #set $rg_string += $format_read_group("\tSM:", $rg_sm)
6 #set $rg_string += "\tLB:" + str($rg.LB) 6 #set $rg_string += $format_read_group("\tPL:", $rg_pl)
7 #end if 7 #set $rg_string += $format_read_group("\tLB:", $rg_lb)
8 #if $rg.CN 8 #set $rg_string += $format_read_group("\tCN:", $rg_cn)
9 #set $rg_string += "\tCN:" + str($rg.CN) 9 #set $rg_string += $format_read_group("\tDS:", $rg_ds)
10 #end if 10 #set $rg_string += $format_read_group("\tDT:", $rg_dt)
11 #if $rg.DS 11 #set $rg_string += $format_read_group("\tFO:", $rg_fo)
12 #set $rg_string += "\tDS:" + str($rg.DS) 12 #set $rg_string += $format_read_group("\tKS:", $rg_ks)
13 #end if 13 #set $rg_string += $format_read_group("\tPG:", $rg_pg)
14 #if $rg.DT 14 #set $rg_string += $format_read_group("\tPI:", $rg_pi)
15 #set $rg_string += "\tDT:" + str($rg.DT) 15 #set $rg_string += $format_read_group("\tPU:", $rg_pu)
16 #end if
17 #if $rg.FO
18 #set $rg_string += "\tFO:" + str($rg.FO)
19 #end if
20 #if $rg.KS
21 #set $rg_string += "\tKS:" + str($rg.KS)
22 #end if
23 #if $rg.PG
24 #set $rg_string += "\tPG:" + str($rg.PG)
25 #end if
26 #if str($rg.PI)
27 #set $rg_string += "\tPI:" + str($rg.PI)
28 #end if
29 #if $rg.PU
30 #set $rg_string += "\tPU:" + str($rg.PU)
31 #end if
32 </token> 16 </token>
33 17
34 <token name="@RG@"> 18 <token name="@RG@">
35 ----- 19 -----
36 20
106 90
107 Dataset collections are in beta-testing. Extensive documentation will be added later this Spring. 91 Dataset collections are in beta-testing. Extensive documentation will be added later this Spring.
108 92
109 93
110 </token> 94 </token>
111 <xml name="readgroup_params">
112 <conditional name="rg">
113 <param name="rg_selector" type="select" label="Set read groups information?" help="(-R in bwa mem; -r in bwa aln); Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets. See help below for more details">
114 <option value="set">Set</option>
115 <option value="do_not_set" selected="True">Do not set</option>
116 </param>
117 <when value="set">
118 <param name="ID" type="text" value="" size="20" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment">
119 <validator type="empty_field" />
120 </param>
121 <param name="SM" type="text" value="" size="20" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" />
122 <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)">
123 <option value="CAPILLARY">CAPILLARY</option>
124 <option value="LS454">LS454</option>
125 <option selected="True" value="ILLUMINA">ILLUMINA</option>
126 <option value="SOLID">SOLID</option>
127 <option value="HELICOS">HELICOS</option>
128 <option value="IONTORRENT">IONTORRENT</option>
129 <option value="PACBIO">PACBIO</option>
130 </param>
131 <param name="LB" type="text" size="25" label="Library name (LB)" />
132 <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" />
133 <param name="DS" type="text" size="25" label="Description (DS)" />
134 <param name="DT" type="text" size="25" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" />
135 <param name="FO" type="text" size="25" optional="true" label="Flow order (FO)" help="The array of nucleotide bases that correspond to the nucleotides used for each flow of each read. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by various other characters. Format: /\*|[ACMGRSVTWYHKDBN]+/">
136 <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator>
137 </param>
138 <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" />
139 <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" />
140 <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" />
141 <param name="PU" type="text" size="25" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" />
142 </when>
143 <when value="do_not_set">
144 <!-- do nothing -->
145 </when>
146 </conditional>
147 </xml>
148 95
149 </macros> 96 </macros>