Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.seqs.xml @ 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 04 Dec 2012 11:05:19 -0600 |
parents | 370b3fc4e7d3 |
children | 95d75b35e4d2 |
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7 | 1 <tool id="mothur_get_seqs" name="Get.seqs" version="1.20.0"> |
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2 <description>Picks sequences by name</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 #import re, os.path |
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6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
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7 ## adds .pick before the last extension to the input file (except align.report) |
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8 --cmd='get.seqs' |
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9 --outputdir='$logfile.extra_files_path' |
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10 --accnos=$accnos |
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11 #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: |
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12 --fasta=$fasta_in |
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13 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] |
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14 #end if |
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15 #if $qfile_in.__str__ != "None" and len($qfile_in.__str__) > 0: |
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16 --qfile=$qfile_in |
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17 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($qfile_in.__str__)) + ":'" + $qfile_out.__str__] |
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18 #end if |
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19 #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: |
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20 --name=$name_in |
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21 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] |
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22 $dups |
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23 #end if |
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24 #if $group_in.__str__ != "None" and len($group_in.__str__) > 0: |
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25 --group=$group_in |
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26 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] |
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27 #end if |
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28 #if $alignreport_in.__str__ != "None" and len($alignreport_in.__str__) > 0: |
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29 --alignreport=$alignreport_in |
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30 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.pick.align.report',$os.path.basename($alignreport_in.__str__)) + ":'" + $alignreport_out.__str__] |
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31 #end if |
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32 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: |
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33 --list=$list_in |
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34 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] |
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35 #end if |
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36 #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: |
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37 --taxonomy=$taxonomy_in |
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38 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] |
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39 #end if |
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40 --result=#echo ','.join($results) |
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41 </command> |
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42 <inputs> |
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43 <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/> |
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44 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> |
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45 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/> |
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46 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
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47 <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/> |
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48 <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/> |
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49 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> |
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50 <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> |
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51 <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/> |
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52 </inputs> |
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53 <outputs> |
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54 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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55 <!-- format should be set to match input --> |
4 | 56 <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> |
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57 <filter>fasta_in != None</filter> |
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58 </data> |
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59 <!-- format should be set to match input --> |
4 | 60 <data format_source="qfile_in" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile"> |
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61 <filter>qfile_in != None</filter> |
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62 </data> |
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63 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.names"> |
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64 <filter>name_in != None</filter> |
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65 </data> |
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66 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"> |
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67 <filter>group_in != None</filter> |
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68 </data> |
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69 <data format="align.report" name="alignreport_out" label="${tool.name} on ${on_string}: pick.align.report"> |
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70 <filter>alignreport_in != None</filter> |
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71 </data> |
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72 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> |
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73 <filter>list_in != None</filter> |
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74 </data> |
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75 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> |
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76 <filter>taxonomy_in != None</filter> |
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77 </data> |
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78 </outputs> |
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79 <requirements> |
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80 <requirement type="package" version="1.27">mothur</requirement> |
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81 </requirements> |
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82 <tests> |
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83 </tests> |
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84 <help> |
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85 **Mothur Overview** |
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86 |
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87 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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88 in the Department of Microbiology and Immunology at The University of Michigan, |
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89 provides bioinformatics for the microbial ecology community. |
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90 |
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91 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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92 |
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93 **Command Documenation** |
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94 |
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95 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. |
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96 |
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97 .. _name: http://www.mothur.org/wiki/Name_file |
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98 .. _group: http://www.mothur.org/wiki/Group_file |
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99 .. _list: http://www.mothur.org/wiki/List_file |
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100 .. _align.report: http://www.mothur.org/wiki/Align.seqs |
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101 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline |
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102 .. _list.seqs: http://www.mothur.org/wiki/list.seqs |
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103 .. _get.seqs: http://www.mothur.org/wiki/Get.seqs |
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104 |
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105 </help> |
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106 </tool> |