Mercurial > repos > devteam > bwa
diff bwa_macros.xml @ 5:fbf460831036 draft
planemo upload commit d0e3412c58bd3bdc1a483a1e2f7f9c2aa5c87a1f-dirty
author | devteam |
---|---|
date | Tue, 21 Jul 2015 13:51:02 -0400 |
parents | ac30bfd3e2a8 |
children | 09a7281d24c5 |
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--- a/bwa_macros.xml Thu Jun 18 17:35:40 2015 -0400 +++ b/bwa_macros.xml Tue Jul 21 13:51:02 2015 -0400 @@ -1,34 +1,18 @@ <macros> - + <import>read_group_macros.xml</import> <token name="@set_rg_string@"> - #set $rg_string = "@RG\tID:" + str($rg.ID) + "\tSM:" + str($rg.SM) + "\tPL:" + str($rg.PL) - #if $rg.LB - #set $rg_string += "\tLB:" + str($rg.LB) - #end if - #if $rg.CN - #set $rg_string += "\tCN:" + str($rg.CN) - #end if - #if $rg.DS - #set $rg_string += "\tDS:" + str($rg.DS) - #end if - #if $rg.DT - #set $rg_string += "\tDT:" + str($rg.DT) - #end if - #if $rg.FO - #set $rg_string += "\tFO:" + str($rg.FO) - #end if - #if $rg.KS - #set $rg_string += "\tKS:" + str($rg.KS) - #end if - #if $rg.PG - #set $rg_string += "\tPG:" + str($rg.PG) - #end if - #if str($rg.PI) - #set $rg_string += "\tPI:" + str($rg.PI) - #end if - #if $rg.PU - #set $rg_string += "\tPU:" + str($rg.PU) - #end if + #set $rg_string = "@RG\tID:" + str($rg_id) + #set $rg_string += $format_read_group("\tSM:", $rg_sm) + #set $rg_string += $format_read_group("\tPL:", $rg_pl) + #set $rg_string += $format_read_group("\tLB:", $rg_lb) + #set $rg_string += $format_read_group("\tCN:", $rg_cn) + #set $rg_string += $format_read_group("\tDS:", $rg_ds) + #set $rg_string += $format_read_group("\tDT:", $rg_dt) + #set $rg_string += $format_read_group("\tFO:", $rg_fo) + #set $rg_string += $format_read_group("\tKS:", $rg_ks) + #set $rg_string += $format_read_group("\tPG:", $rg_pg) + #set $rg_string += $format_read_group("\tPI:", $rg_pi) + #set $rg_string += $format_read_group("\tPU:", $rg_pu) </token> <token name="@RG@"> @@ -108,42 +92,5 @@ </token> - <xml name="readgroup_params"> - <conditional name="rg"> - <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"> - <option value="set">Set</option> - <option value="do_not_set" selected="True">Do not set</option> - </param> - <when value="set"> - <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"> - <validator type="empty_field" /> - </param> - <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" /> - <param name="PL" type="select" label="Platform/technology used to produce the reads (PL)"> - <option value="CAPILLARY">CAPILLARY</option> - <option value="LS454">LS454</option> - <option selected="True" value="ILLUMINA">ILLUMINA</option> - <option value="SOLID">SOLID</option> - <option value="HELICOS">HELICOS</option> - <option value="IONTORRENT">IONTORRENT</option> - <option value="PACBIO">PACBIO</option> - </param> - <param name="LB" type="text" size="25" label="Library name (LB)" /> - <param name="CN" type="text" size="25" label="Sequencing center that produced the read (CN)" /> - <param name="DS" type="text" size="25" label="Description (DS)" /> - <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" /> - <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]+/"> - <validator type="regex" message="Invalid flow order">\*|[ACMGRSVTWYHKDBN]+$</validator> - </param> - <param name="KS" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> - <param name="PG" type="text" size="25" label="Programs used for processing the read group (PG)" /> - <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> - <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)" /> - </when> - <when value="do_not_set"> - <!-- do nothing --> - </when> - </conditional> - </xml> </macros>