Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/screen.seqs.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
author | Jim Johnson <jj@umn.edu> |
---|---|
date | Tue, 30 Jul 2013 09:26:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
line wrap: on
line source
<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.23.0"> <description>Screen sequences</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path --cmd='screen.seqs' #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_fasta.__str__)) + ":'" + $out_file.__str__] #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.bad.accnos',$os.path.basename($input_fasta.__str__)) + ":'" + $bad_accnos.__str__] --outputdir='$logfile.extra_files_path' --tmpdir='${logfile.extra_files_path}/input' --fasta=$input_fasta #if int($start) >= 0: --start=$start #end if #if int($end) >= 0: --end=$end #end if #if int($minlength) >= 0: --minlength=$minlength #end if #if int($maxlength) >= 0: --maxlength=$maxlength #end if #if int($maxambig) >= 0: --maxambig=$maxambig #end if #if int($maxhomop) >= 0: --maxhomop=$maxhomop #end if #if int($criteria) >= 0: --criteria=$criteria #end if #if $optimize != None and $optimize.__str__ != "None": --optimize=$optimize #end if #if $input_qfile != None and $input_qfile.__str__ != "None": --qfile=$input_qfile #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_qfile.__str__)) + ":'" + $output_qfile.__str__] #end if #if $input_names != None and $input_names.__str__ != "None": --name=$input_names #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_names.__str__)) + ":'" + $output_names.__str__] #end if #if $input_groups != None and $input_groups.__str__ != "None": --group=$input_groups #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_groups.__str__)) + ":'" + $output_groups.__str__] #end if #if $input_alignreport != None and $input_alignreport.__str__ != "None": --alignreport=$input_alignreport ###set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_alignreport.__str__)) + ":'" + $output_alignreport.__str__] #set results = $results + ["'^\S+\.good\.align\.report$:'" + $output_alignreport.__str__] #end if #if $input_taxonomy != None and $input_taxonomy.__str__ != "None": --taxonomy=$input_taxonomy #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.good.\2',$os.path.basename($input_taxonomy.__str__)) + ":'" + $output_taxonomy.__str__] #end if --result=#echo ','.join($results) --processors=8 </command> <inputs> <param name="input_fasta" type="data" format="fasta,align" label="fasta - Fasta to screen"/> <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/> <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/> <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/> <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/> <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/> <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/> <param name="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained(ignored when negative)"/> <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters"> <option value="start">start</option> <option value="end">end</option> <option value="minlength">minlength</option> <option value="maxlength">maxlength</option> <option value="maxambig">maxambig</option> <option value="maxhomop">maxhomop</option> </param> <param name="input_qfile" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/> <param name="input_names" type="data" format="names" optional="true" label="name - Sequence Names to screen"/> <param name="input_groups" type="data" format="groups" optional="true" label="group - Groups to screen"/> <param name="input_alignreport" type="data" format="align.report" optional="true" label="alignreport - Align Report to screen"/> <param name="input_taxonomy" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format_source="input_fasta" name="out_file" label="${tool.name} on ${on_string}: good.${input_fasta.datatype.file_ext}" /> <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" /> <data format_source="input_qfile" name="output_qfile" label="${tool.name} on ${on_string}: qfile" > <filter>input_qfile != None</filter> </data> <data format="names" name="output_names" label="${tool.name} on ${on_string}: names" > <filter>input_names != None</filter> </data> <data format="groups" name="output_groups" label="${tool.name} on ${on_string}: groups" > <filter>input_groups != None</filter> </data> <data format="align.report" name="output_alignreport" label="${tool.name} on ${on_string}: align.report" > <filter>input_alignreport != None</filter> </data> <data format="taxonomy" name="output_taxonomy" label="${tool.name} on ${on_string}: taxonomy" > <filter>input_taxonomy != None</filter> </data> </outputs> <requirements> <requirement type="package" version="1.27">mothur</requirement> </requirements> <tests> </tests> <help> **Mothur Overview** Mothur_, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan, provides bioinformatics for the microbial ecology community. .. _Mothur: http://www.mothur.org/wiki/Main_Page **Command Documenation** The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file. .. _name: http://www.mothur.org/wiki/Name_file .. _group: http://www.mothur.org/wiki/Group_file .. _align.report: http://www.mothur.org/wiki/Align.seqs .. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs </help> </tool>