Mercurial > repos > jjohnson > mothur_toolsuite
comparison mothur/tools/mothur/remove.seqs.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
| author | jjohnson |
|---|---|
| date | Tue, 07 Jun 2011 17:35:35 -0400 |
| parents | 3202a38e44d9 |
| children | e990ac8a0f58 |
comparison
equal
deleted
inserted
replaced
| 0:3202a38e44d9 | 1:fcc0778f6987 |
|---|---|
| 1 <tool id="mothur_remove_seqs" name="Remove.seqs" version="1.15.0"> | 1 <tool id="mothur_remove_seqs" name="Remove.seqs" version="1.16.0"> |
| 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$:'" + $logfile.__str__] | 6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
| 39 #end if | 39 #end if |
| 40 --result=#echo ','.join($results) | 40 --result=#echo ','.join($results) |
| 41 </command> | 41 </command> |
| 42 <inputs> | 42 <inputs> |
| 43 <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/> | 43 <param name="accnos" type="data" format="accnos" label="accnos - Accession Names"/> |
| 44 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> | 44 <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/> |
| 45 <param name="qfile_in" type="data" format="qual" 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="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 ${on_string}: logfile" /> |
| 55 <!-- format should be set to match input --> | 55 <!-- format should be set to match input --> |
| 56 <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> | 56 <!-- There should be a format_source attribute |
| 57 <data format_source="fasta_in" metadata_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.${fasta_in.datatype.file_ext}"> | |
| 57 <filter>fasta_in != None</filter> | 58 <filter>fasta_in != None</filter> |
| 59 </data> | |
| 60 --> | |
| 61 <data format="fasta" metadata_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.${fasta_in.datatype.file_ext}"> | |
| 62 <filter>fasta_in != None</filter> | |
| 63 <change_format> | |
| 64 <when input="${fasta_in.datatype.file_ext}" value="align" format="align" /> | |
| 65 </change_format> | |
| 58 </data> | 66 </data> |
| 59 <!-- format should be set to match input --> | 67 <!-- format should be set to match input --> |
| 60 <data format="qual" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile"> | 68 <data format="qual" name="qfile_out" label="${tool.name} on ${on_string}: pick.qfile"> |
| 61 <filter>qfile_in != None</filter> | 69 <filter>qfile_in != None</filter> |
| 70 <change_format> | |
| 71 <when input="${qfile_in.datatype.file_ext}" value="qual454" format="qual454" /> | |
| 72 </change_format> | |
| 62 </data> | 73 </data> |
| 63 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.names"> | 74 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.names"> |
| 64 <filter>name_in != None</filter> | 75 <filter>name_in != None</filter> |
| 65 </data> | 76 </data> |
| 66 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"> | 77 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"> |