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comparison qiime/per_library_stats.xml @ 0:003162f90751 draft

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author azuzolo
date Wed, 06 Jun 2012 16:40:30 -0400
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1 <tool id="per_library_stats" name="per_library_stats" version="2.0.0">
2 <description>Calculate per library statistics</description>
3 <requirements>
4 <requirement type="binary">per_library_stats.py</requirement>
5 </requirements>
6 <command interpreter="python">
7 qiime_wrapper.py
8 per_library_stats.py
9 --otu_table_fp=$otu_table_fp
10 #if $mapfile != None and $mapfile.__str__ != 'None' and $mapfile.__str__ != '':
11 --mapfile=$mapfile
12 #end if
13 --outputfile=$outputfile
14 </command>
15 <inputs>
16 <param name="otu_table_fp" type="data" format="txt" label="otu_table_fp"
17 help="path to the input OTU table (i.e., the output from make_otu_table.py) [REQUIRED]"/>
18 <param name="mapfile" type="data" optional="true" format="txt" label="mapfile" help="A mapping file. If included, this script will modify the mapping file to include sequences per sample (library) information, and write the modified mapping file to the output file. [OPTIONAL]"/>
19 </inputs>
20 <outputs>
21 <data format="txt" name="outputfile" label="${tool.name} on ${on_string}"/>
22 </outputs>
23 <tests>
24 </tests>
25 <help>.. class:: warningmark Warning: log data from standard output currently not available.
26
27 For more information, see per_library_stats_ in the Qiime documentation.
28
29 Updated and validated 01/18/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA
30
31 Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN
32
33 .. _per_library_stats: http://qiime.org/scripts/per_library_stats.html</help>
34 </tool>
35