Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/screen.seqs.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
parents | 3202a38e44d9 |
children | e990ac8a0f58 |
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<tool id="mothur_screen_seqs" name="Screen.seqs" version="1.16.0"> <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.__str__)) + ":'" + $out_file.__str__] #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.bad.accnos',$os.path.basename($input.__str__)) + ":'" + $bad_accnos.__str__] --outputdir='$logfile.extra_files_path' --tmpdir='${logfile.extra_files_path}/input' --fasta=$input #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_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__)) + ":'" + $output_alignreport.__str__] #end if --result=#echo ','.join($results) --processors=2 </command> <inputs> <param name="input" 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_names" type="data" format="names" optional="true" label="name - Sequece 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"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="fasta" name="out_file" label="${tool.name} on ${on_string}: good.${input.datatype.file_ext}" > <change_format> <when input_dataset="input" attribute="ext" value="align" format="align"/> </change_format> </data> <data format="accnos" name="bad_accnos" label="${tool.name} on ${on_string}: bad.accnos" /> <data format="names" name="output_names" label="${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> </outputs> <requirements> <requirement type="binary">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 names, group, or align.report file. .. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs </help> </tool>