Mercurial > repos > jjohnson > mothur_toolsuite

annotate mothur/tools/mothur/summary.seqs.xml @ 3:6b358d0f17b4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Update to Mothur version 1.24
author Jim Johnson <jj@umn.edu>
date Wed, 05 Sep 2012 19:49:43 -0500
parents e076d95dbdb5
children a9d51d14f9e9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
1 <tool id="mothur_summary_seqs" name="Summary.seqs" version="1.19.0">
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
2 <description>Summarize the quality of sequences</description>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
3 <command interpreter="python">
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
4 mothur_wrapper.py
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
5 --cmd='summary.seqs'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.summary$:'$out_summary
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
7 --outputdir='$logfile.extra_files_path'
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
8 --fasta=$fasta
2
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
9 #if $name.__str__ != "None" and len($name.__str__) > 0:
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
10 --name=$name
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
11 #end if
3
6b358d0f17b4 Update to Mothur version 1.24
Jim Johnson <jj@umn.edu>
parents: 2
diff changeset
12 --processors=8
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
13 </command>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
14 <inputs>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
15 <param name="fasta" type="data" format="fasta,align" label="fasta - Dataset"/>
2
e076d95dbdb5 Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
jjohnson
parents: 1
diff changeset
16 <param name="name" type="data" format="names" label="name - Names" optional="true"/>
0
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
17 </inputs>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
18 <outputs>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
19 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" />
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
20 <data format="summary" name="out_summary" label="${tool.name} on ${on_string}: summary" />
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
21 </outputs>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
22 <requirements>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
23 <requirement type="binary">mothur</requirement>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
24 </requirements>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
25 <tests>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
26 </tests>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
27 <help>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
28 **Mothur Overview**
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
29
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
30 Mothur_, initiated by Dr. Patrick Schloss and his software development team
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
31 in the Department of Microbiology and Immunology at The University of Michigan,
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
32 provides bioinformatics for the microbial ecology community.
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
33
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
34 .. _Mothur: http://www.mothur.org/wiki/Main_Page
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
35
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
36 **Command Documenation**
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
37
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
38 The summary.seqs_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
39
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
40
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
41 .. _summary.seqs: http://www.mothur.org/wiki/Summary.seqs
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
42
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
43 </help>
591e72edabed Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
jjohnson
parents:
diff changeset
44 </tool>