Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.seqs.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
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<tool id="mothur_get_seqs" name="Get.seqs" version="1.20.0"> <description>Picks sequences by name</description> <command interpreter="python"> mothur_wrapper.py #import re, os.path #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] ## adds .pick before the last extension to the input file (except align.report) --cmd='get.seqs' --outputdir='$logfile.extra_files_path' --accnos=$accnos #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: --fasta=$fasta_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] #end if #if $qfile_in.__str__ != "None" and len($qfile_in.__str__) > 0: --qfile=$qfile_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($qfile_in.__str__)) + ":'" + $qfile_out.__str__] #end if #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: --name=$name_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] $dups #end if #if $group_in.__str__ != "None" and len($group_in.__str__) > 0: --group=$group_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] #end if #if $alignreport_in.__str__ != "None" and len($alignreport_in.__str__) > 0: --alignreport=$alignreport_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.pick.align.report',$os.path.basename($alignreport_in.__str__)) + ":'" + $alignreport_out.__str__] #end if #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: --list=$list_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] #end if #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: --taxonomy=$taxonomy_in #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] #end if --result=#echo ','.join($results) </command> <inputs> <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/> <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/> <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/> <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <!-- format should be set to match input --> <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> <filter>fasta_in != None</filter> </data> <!-- format should be set to match input --> <data format_source="qfile_in" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile"> <filter>qfile_in != None</filter> </data> <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.names"> <filter>name_in != None</filter> </data> <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"> <filter>group_in != None</filter> </data> <data format="align.report" name="alignreport_out" label="${tool.name} on ${on_string}: pick.align.report"> <filter>alignreport_in != None</filter> </data> <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> <filter>list_in != None</filter> </data> <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> <filter>taxonomy_in != 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 get.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection. .. _name: http://www.mothur.org/wiki/Name_file .. _group: http://www.mothur.org/wiki/Group_file .. _list: http://www.mothur.org/wiki/List_file .. _align.report: http://www.mothur.org/wiki/Align.seqs .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline .. _list.seqs: http://www.mothur.org/wiki/list.seqs .. _get.seqs: http://www.mothur.org/wiki/Get.seqs </help> </tool>