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view read_group_macros.xml @ 4:774491f4a074 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/bwa commit 33c17fa6a2d8c15972d93031b2ca4182cdf31439
author | devteam |
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date | Thu, 01 Jun 2017 11:38:11 -0400 |
parents | c9c78719ef26 |
children | 086ba7b646e5 |
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<macros> <!-- Import this at the top of your command block and then define rg_auto_name. --> <token name="@define_read_group_helpers@"> #def identifier_or_name($input1) #if hasattr($input1, 'element_identifier') #return $input1.element_identifier #else #return $input1.name.rstrip('.gz').rstrip('.fastq').rstrip('.fq') #end if #end def #def clean(name) #import re #set $name_clean = re.sub('[^\w\-_\.]', '_', $name) #return $name_clean #end def #def read_group_name_default($input1, $input2=None) #if $input2 is None #return $clean($identifier_or_name($input1)) #else #import itertools #set $input_name1 = $clean($identifier_or_name($input1)) #set $input_name2 = $clean($identifier_or_name($input2)) #set $common_prefix = ''.join([c[0] for c in itertools.takewhile(lambda x: all(x[0] == y for y in x), itertools.izip(*[$input_name1, $input_name2]))]) #if len($common_prefix) > 3 #return $common_prefix #else #return $input_name1 #end if #end if #end def #def format_read_group(prefix, value, quote='', arg='') #if $value #return $arg + $quote + $prefix + $value + $quote #else #return '' #end if #end def #def rg_param(name) #if $varExists("rg") #return $rg.get($name, None) #else #return $getVar($name, None) #end if #end def #set $use_rg = True </token> <!-- preconditions use_rg and rg_auto_name have been defined. --> <token name="@set_read_group_vars@"> #if $use_rg #if $rg_param('read_group_id_conditional') is None #set $rg_id = $rg_auto_name #elif $rg_param('read_group_id_conditional').do_auto_name #set $rg_id = $rg_auto_name #else #set $rg_id = str($rg_param('read_group_id_conditional').ID) #end if #if $rg_param('read_group_sm_conditional') is None #set $rg_sm = '' #elif $rg_param('read_group_sm_conditional').do_auto_name #set $rg_sm = $rg_auto_name #else #set $rg_sm = str($rg_param('read_group_sm_conditional').SM) #end if #if $rg_param('PL') #set $rg_pl = str($rg_param('PL')) #else #set $rg_pl = '' #end if #if $rg_param('read_group_lb_conditional') is None #set $rg_lb = '' #elif $rg_param('read_group_lb_conditional').do_auto_name #set $rg_lb = $rg_auto_name #else #set $rg_lb = str($rg_param('read_group_lb_conditional').LB) #end if #if $rg_param('CN') #set $rg_cn = str($rg_param('CN')) #else #set $rg_cn = '' #end if #if $rg_param("DS") #set $rg_ds = str($rg_param("DS")) #else #set $rg_ds = '' #end if #if $rg_param("DT") #set $rg_dt = str($rg_param("DT")) #else #set $rg_dt = '' #end if #if $rg_param("FO") #set $rg_fo = str($rg_param("FO")) #else #set $rg_fo = '' #end if #if $rg_param("KS") #set $rg_ks = str($rg_param("KS")) #else #set $rg_ks = '' #end if #if $rg_param("PG") #set $rg_pg = str($rg_param("PG")) #else #set $rg_pg = '' #end if #if $rg_param("PI") != None #set $rg_pi = str($rg_param("PI")) #else #set $rg_pi = '' #end if #if $rg_param("PU") #set $rg_pu = str($rg_param("PU")) #else #set $rg_pu = '' #end if #end if </token> <token name="@set_use_rg_var@"> #set $use_rg = str($rg.rg_selector) != "do_not_set" </token> <xml name="read_group_auto_name_conditional"> <param name="do_auto_name" type="boolean" label="Auto-assign" help="Use dataset name or collection information to automatically assign this value" checked="no" /> <when value="true"> </when> <when value="false"> <yield /> </when> </xml> <xml name="read_group_id_param"> <param name="ID" type="text" value="" label="Read group identifier (ID)" help="This value must be unique among multiple samples in your experiment" optional="false"> <validator type="empty_field" /> </param> </xml> <xml name="read_group_id_conditional"> <conditional name="read_group_id_conditional"> <expand macro="read_group_auto_name_conditional"> <expand macro="read_group_id_param" /> </expand> </conditional> </xml> <xml name="read_group_sm_param"> <param name="SM" type="text" value="" label="Read group sample name (SM)" help="This value should be descriptive. Use pool name where a pool is being sequenced" /> </xml> <xml name="read_group_sm_conditional"> <conditional name="read_group_sm_conditional"> <expand macro="read_group_auto_name_conditional"> <expand macro="read_group_sm_param" /> </expand> </conditional> </xml> <!-- Above SM param is optional (for SAM/BAM spec, this is required as per Picard. --> <xml name="read_group_sm_param_required"> <param name="SM" type="text" value="" label="Read group sample name (SM)" optional="false" help="This value should be descriptive. Use pool name where a pool is being sequenced"> <validator type="empty_field" /> </param> </xml> <xml name="read_group_sm_required_conditional"> <conditional name="read_group_sm_conditional"> <expand macro="read_group_auto_name_conditional"> <expand macro="read_group_sm_param" /> </expand> </conditional> </xml> <xml name="read_group_pl_param"> <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> </xml> <xml name="read_group_lb_param"> <param name="LB" type="text" label="Library name (LB)" optional="true" /> </xml> <xml name="read_group_lb_conditional"> <conditional name="read_group_lb_conditional"> <expand macro="read_group_auto_name_conditional"> <expand macro="read_group_lb_param" /> </expand> </conditional> </xml> <xml name="read_group_lb_required_param"> <param name="LB" type="text" label="Library name (LB)" optional="false"> <validator type="empty_field" /> </param> </xml> <xml name="read_group_lb_required_conditional"> <conditional name="read_group_lb_conditional"> <expand macro="read_group_auto_name_conditional"> <expand macro="read_group_lb_required_param" /> </expand> </conditional> </xml> <xml name="read_group_cn_param"> <param name="CN" type="text" label="Sequencing center that produced the read (CN)" /> </xml> <xml name="read_group_ds_param"> <param name="DS" type="text" label="Description (DS)" /> </xml> <xml name="read_group_dt_param"> <param name="DT" type="text" label="Date that run was produced (DT)" help="ISO8601 format date or date/time, like YYYY-MM-DD" /> </xml> <xml name="read_group_fo_param"> <param name="FO" type="text" 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> </xml> <xml name="read_group_ks_param"> <param name="KS" type="text" label="The array of nucleotide bases that correspond to the key sequence of each read (KS)" /> </xml> <xml name="read_group_pg_param"> <param name="PG" type="text" label="Programs used for processing the read group (PG)" /> </xml> <xml name="read_group_pi_param"> <param name="PI" type="integer" optional="true" label="Predicted median insert size (PI)" /> </xml> <xml name="read_group_pu_param"> <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="True" /> </xml> <xml name="read_group_pu_required_param"> <param name="PU" type="text" label="Platform unit (PU)" help="Unique identifier (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)" optional="False" /> </xml> <!-- Only ID is required - all groups available --> <xml name="read_group_inputs_spec"> <expand macro="read_group_id_conditional" /> <expand macro="read_group_sm_conditional" /> <expand macro="read_group_pl_param" /> <expand macro="read_group_lb_conditional" /> <expand macro="read_group_cn_param" /> <expand macro="read_group_ds_param" /> <expand macro="read_group_dt_param" /> <expand macro="read_group_fo_param" /> <expand macro="read_group_ks_param" /> <expand macro="read_group_pg_param" /> <expand macro="read_group_pi_param" /> <expand macro="read_group_pu_param" /> </xml> <!-- ID, SM, LB, PU, PL all required - not ks, pg, or fo params. --> <xml name="read_group_inputs_picard"> <expand macro="read_group_id_conditional" /> <expand macro="read_group_sm_required_conditional" /> <expand macro="read_group_lb_required_conditional" /> <expand macro="read_group_pl_param" /> <expand macro="read_group_pu_required_param" /> <expand macro="read_group_cn_param" /> <expand macro="read_group_ds_param" /> <expand macro="read_group_pi_param" /> <expand macro="read_group_dt_param" /> </xml> <xml name="read_group_conditional"> <conditional name="rg"> <param name="rg_selector" type="select" label="Set read groups information?" help="Specifying read group information can greatly simplify your downstream analyses by allowing combining multiple datasets."> <option value="set">Set read groups (SAM/BAM specification)</option> <option value="set_picard">Set read groups (Picard style)</option> <option value="set_id_auto">Automatically assign ID</option> <option value="do_not_set" selected="True">Do not set</option> </param> <when value="set_picard"> <expand macro="read_group_inputs_picard" /> </when> <when value="set"> <expand macro="read_group_inputs_spec" /> </when> <when value="set_id_auto"> </when> <when value="do_not_set"> </when> </conditional> </xml> </macros>