Mercurial > repos > devteam > bwa
comparison bwa_macros.xml @ 5:fbf460831036 draft
planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
author | devteam |
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date | Tue, 21 Jul 2015 13:51:02 -0400 |
parents | ac30bfd3e2a8 |
children | 09a7281d24c5 |
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4:ac30bfd3e2a8 | 5:fbf460831036 |
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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> |