Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/remove.lineage.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_lineage" name="Remove.lineage" version="1.16.0"> | 1 <tool id="mothur_remove_lineage" name="Remove.lineage" version="1.19.0"> |
2 <description>Picks by taxon</description> | 2 <description>Picks by taxon</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$:'" + $logfile.__str__] | 6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
18 --group=$group_in | 18 --group=$group_in |
19 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] | 19 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] |
20 #end if | 20 #end if |
21 #if $alignreport_in.__str__ != "None" and len($alignreport_in.__str__) > 0: | 21 #if $alignreport_in.__str__ != "None" and len($alignreport_in.__str__) > 0: |
22 --alignreport=$alignreport_in | 22 --alignreport=$alignreport_in |
23 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($alignreport_in.__str__)) + ":'" + $alignreport_out.__str__] | 23 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.pick.align.report',$os.path.basename($alignreport_in.__str__)) + ":'" + $alignreport_out.__str__] |
24 #end if | 24 #end if |
25 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: | 25 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: |
26 --list=$list_in | 26 --list=$list_in |
27 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] | 27 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] |
28 #end if | 28 #end if |
32 $dups | 32 $dups |
33 #end if | 33 #end if |
34 --result=#echo ','.join($results) | 34 --result=#echo ','.join($results) |
35 </command> | 35 </command> |
36 <inputs> | 36 <inputs> |
37 <param name="taxonomy" type="data" format="taxonomy" label="taxonomy - Taxonomy"/> | 37 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/> |
38 <param name="taxons" type="select" size="120" label="Browse Taxons from Taxonomy"> | 38 <param name="taxons" type="select" size="120" label="Browse Taxons from Taxonomy"> |
39 <options from_dataset="taxonomy"> | 39 <options from_dataset="taxonomy"> |
40 <column name="name" index="1"/> | 40 <column name="name" index="1"/> |
41 <column name="value" index="1"/> | 41 <column name="value" index="1"/> |
42 <filter type="unique_value" name="unique_taxon" column="1" /> | 42 <filter type="unique_value" name="unique_taxon" column="1" /> |
51 <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/> | 51 <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/> |
52 </inputs> | 52 </inputs> |
53 <outputs> | 53 <outputs> |
54 <!-- fix format --> | 54 <!-- fix format --> |
55 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> | 55 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
56 <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/> | 56 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/> |
57 <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> | 57 <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> |
58 <filter>fasta_in != None</filter> | 58 <filter>fasta_in != None</filter> |
59 </data> | 59 </data> |
60 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.group"> | 60 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.group"> |
61 <filter>group_in != None</filter> | 61 <filter>group_in != None</filter> |
84 | 84 |
85 .. _Mothur: http://www.mothur.org/wiki/Main_Page | 85 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
86 | 86 |
87 **Command Documenation** | 87 **Command Documenation** |
88 | 88 |
89 The remove.lineage_ command reads a taxonomy file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta, name, group, list, or align.report file to this command and mothur will generate new files for each of those containing only the selected sequences. | 89 The remove.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are not from that taxon. You may also include either a fasta_, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences. |
90 | 90 |
91 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline | |
92 .. _name: http://www.mothur.org/wiki/Name_file | |
93 .. _group: http://www.mothur.org/wiki/Group_file | |
94 .. _list: http://www.mothur.org/wiki/List_file | |
95 .. _align.report: http://www.mothur.org/wiki/Align.seqs | |
91 .. _remove.lineage: http://www.mothur.org/wiki/Remove.lineage | 96 .. _remove.lineage: http://www.mothur.org/wiki/Remove.lineage |
92 | 97 |
93 | 98 |
94 </help> | 99 </help> |
95 </tool> | 100 </tool> |