Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/remove.seqs.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 5265aa9067e0 |
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1:fcc0778f6987 | 2:e990ac8a0f58 |
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1 <tool id="mothur_remove_seqs" name="Remove.seqs" version="1.16.0"> | 1 <tool id="mothur_remove_seqs" name="Remove.seqs" version="1.19.0"> |
2 <description>Remove sequences by name</description> | 2 <description>Remove sequences by name</description> |
3 <command interpreter="python"> | 3 <command interpreter="python"> |
4 mothur_wrapper.py | 4 mothur_wrapper.py |
5 #import re, os.path | 5 #import re, os.path |
6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] | 6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
45 <param name="qfile_in" type="data" format="qual,qual454" optional="true" label="qfile - Fasta Quality"/> | 45 <param name="qfile_in" type="data" format="qual,qual454" optional="true" label="qfile - Fasta Quality"/> |
46 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> | 46 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
47 <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/> | 47 <param name="group_in" type="data" format="groups" optional="true" label="group - Sequences Groups"/> |
48 <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/> | 48 <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/> |
49 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> | 49 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> |
50 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy"/> | 50 <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> |
51 <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/> | 51 <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicates"/> |
52 </inputs> | 52 </inputs> |
53 <outputs> | 53 <outputs> |
54 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 54 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
55 <!-- format should be set to match input --> | 55 <!-- format should be set to match input --> |
81 <filter>alignreport_in != None</filter> | 81 <filter>alignreport_in != None</filter> |
82 </data> | 82 </data> |
83 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> | 83 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> |
84 <filter>list_in != None</filter> | 84 <filter>list_in != None</filter> |
85 </data> | 85 </data> |
86 <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> | 86 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> |
87 <filter>taxonomy_in != None</filter> | 87 <filter>taxonomy_in != None</filter> |
88 </data> | 88 </data> |
89 </outputs> | 89 </outputs> |
90 <requirements> | 90 <requirements> |
91 <requirement type="binary">mothur</requirement> | 91 <requirement type="binary">mothur</requirement> |
101 | 101 |
102 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 102 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
103 | 103 |
104 **Command Documenation** | 104 **Command Documenation** |
105 | 105 |
106 The remove.seqs_ command takes a list of sequence names and either a fasta, name, group, list, or align.report file to generate a new file that does not contain the sequences in the list. This command may be used in conjunction with the list.seqs command to help screen a sequence collection. | 106 The remove.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 does not contain the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection. |
107 | 107 |
108 .. _name: http://www.mothur.org/wiki/Name_file | |
109 .. _group: http://www.mothur.org/wiki/Group_file | |
110 .. _list: http://www.mothur.org/wiki/List_file | |
111 .. _align.report: http://www.mothur.org/wiki/Align.seqs | |
112 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline | |
113 .. _list.seqs: http://www.mothur.org/wiki/list.seqs | |
108 .. _remove.seqs: http://www.mothur.org/wiki/Remove.seqs | 114 .. _remove.seqs: http://www.mothur.org/wiki/Remove.seqs |
109 | 115 |
110 </help> | 116 </help> |
111 </tool> | 117 </tool> |