comparison mothur/tools/mothur/trim.flows.xml @ 31:a3eed59297ea

Patches courtesy of Peter Briggs, Bioinformatics Core Facility University of Manchester make.contigs.xml.patch:# make.contigs.xml.patch make.contigs.xml.patch:# make.contigs.xml.patch:# 1. Fix cosmetic typo in <description> (forard -> forward) make.contigs.xml.patch:# 2. Address error due to having 'mismatch' as the name for both an input and an output parameter: make.contigs.xml.patch:# rename output parameter to 'cmismatch' make.contigs.xml.patch:# 3. Remove 'threshold' parameter: make.contigs in mothur doesn't support a 'threshold' parameter metagenomics.py.patch:# metagenomics.py.patch metagenomics.py.patch:# metagenomics.py.patch:# 1. Groups class: names were being taken from the wrong field (affected shhh.flows tool) metagenomics.py.patch:# 2. Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular metagenomics.py.patch:# data uploads being sniffed as this type mothur_wrapper.py.patch:# mothur_wrapper.py.patch mothur_wrapper.py.patch:# mothur_wrapper.py.patch:# 1. Update 'cmd_dict' settings for shhh.flows and shhh.seqs (otherwise these functions will mothur_wrapper.py.patch:# fail on execution) mothur_wrapper.py.patch:# 2. Fix add_option calls defining '--match' and '--mismatch' command line options (otherwise mothur_wrapper.py.patch:# syntax error causes immediate failure) screen.seqs.xml.patch:# screen.seqs.xml.patch screen.seqs.xml.patch:# screen.seqs.xml.patch:# Replace pattern for align.report output file in definiting of 'results' parameter in screen.seqs.xml.patch:# <command> section (otherwise output_alignreport data item is empty). shhh.flows.xml.patch:# shhh.flows.xml.patch shhh.flows.xml.patch:# shhh.flows.xml.patch:# Replace 'format_source' with 'format' for output parameters (otherwise formats are not shhh.flows.xml.patch:# correctly assigned to output datasets) shhh.seqs.xml.patch:# shhh.seqs.xml.patch shhh.seqs.xml.patch:# shhh.seqs.xml.patch:# 1. Fix patterns in --result (in <command> section) for shhh_seqs.fasta and shhh_seqs.names shhh.seqs.xml.patch:# output files (otherwise files are not collected and associated data items are empty) shhh.seqs.xml.patch:# 2. Replace 'format_source' with 'format' for output parameters (otherwise formats are not shhh.seqs.xml.patch:# correctly assigned to output datasets) trim.flows.xml.patch:# trim.flows.xml.patch trim.flows.xml.patch:# trim.flows.xml.patch:# Remove erroneous space from --result definition in <command> section (otherwise causes tool trim.flows.xml.patch:# failure) trim.seqs.xml.patch:# trim.seqs.xml.patch trim.seqs.xml.patch:# trim.seqs.xml.patch:# 1. Remove reference to undefined 'oligo.allvalues' varible in <command> section (otherwise trim.seqs.xml.patch:# causes failure on execution) trim.seqs.xml.patch:# 2. Fix format for input parameter 'names' (format should be 'names' not 'name') trim.seqs.xml.patch:# 3. Add output parameter 'scrap_names' (to ensure consistent collection of all outputs) trim.seqs.xml.patch:# 4. Update --result definition in <command> section to collect both trim.names and scrap.names

30:a90d1915a176

  mothur_wrapper.py 
  #import re, os.path
  --cmd='trim.flows'
  ## #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  ## #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($flow.__str__)) + ":'" + $trim_flow.__str__]
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.trim\.flow$:'$trim_flow, '^\S+\.scrap\.flow$:'$scrap_flow,'^\S+\.flow\.files$:'$flow_files,'^\S+\.flow\.fasta$:'$flow_fasta
  --outputdir='$logfile.extra_files_path'
  --flow=$flow
  #if $minflows.__str__ != '':
   --minflows=$minflows 
  #end if

31:a3eed59297ea

  mothur_wrapper.py 
  #import re, os.path
  --cmd='trim.flows'
  ## #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__]
  ## #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($flow.__str__)) + ":'" + $trim_flow.__str__]
  --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.trim\.flow$:'$trim_flow,'^\S+\.scrap\.flow$:'$scrap_flow,'^\S+\.flow\.files$:'$flow_files,'^\S+\.flow\.fasta$:'$flow_fasta
  --outputdir='$logfile.extra_files_path'
  --flow=$flow
  #if $minflows.__str__ != '':
   --minflows=$minflows 
  #end if