view mothur/tool-data/mothur_aligndb.loc.sample @ 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

#This is a sample file distributed with Galaxy that enables tools
#to use a directory of metagenomics files.  
#file has this format (white space characters are TAB characters):
#
# Reference Alignments:  http://www.mothur.org/wiki/Alignment_database
#
#<dbname>	<file_base>
#
#greengenes	/project/db/galaxy/mothur/core_set_aligned.imputed.fasta
#silva archaea	/project/db/galaxy/mothur/Silva.archaea/silva.archaea.fasta
#silva bacteria	/project/db/galaxy/mothur/silva.bacteria/silva.bacteria.fasta
#silva eukarya	/project/db/galaxy/mothur/silva.eukarya.fasta
#silva archaea nogap	/project/db/galaxy/mothur/Silva.archaea/nogap.archaea.fasta
#silva bacteria nogap	/project/db/galaxy/mothur/silva.bacteria/nogap.bacteria.fasta
#silva eukarya nogap	/project/db/galaxy/mothur/nogap.eukarya.fasta
#FungiLSU_train_1400bp_8506_mod.fasta	/project/db/galaxy/mothur/RDP/FungiLSU_train_1400bp_8506_mod.fasta
#trainset6_032010.rdp.fasta	/project/db/galaxy/mothur/RDP/trainset6_032010.rdp.fasta
#trainset7_112011.pds.fasta	/project/db/galaxy/mothur/RDP/trainset7_112011.pds.fasta
#trainset7_112011.rdp.fasta	/project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta