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comparison preclassification.xml @ 0:d4690e65afcd draft

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author bcclaywell
date Thu, 26 Feb 2015 18:16:36 -0500
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1 <tool id="PHYLO_preclassification" name="Generate database" version="1.2.0">
2 <description>for classification</description>
3 <requirements>
4 <requirement type="package">yapp_env</requirement>
5 </requirements>
6 <macros>
7 <import>macros.xml</import>
8 </macros>
9 <version_command>echo "guppy $(guppy --version)"</version_command>
10 <command interpreter="bash">
11 preclassification-wrapper.sh ${config}
12 </command>
13 <stdio>
14 <expand macro="basic_errors"/>
15 </stdio>
16 <inputs>
17 <param name="dedup_info" type="data" format="csv" label="Deduplication info"/>
18 <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
19 <param name="nbc_seqs" type="data" format="fasta" label="Query alignment" help="The query alignment specified here should be the same as the one passed to pplacer."/>
20 <param name="placed_seqs" type="data" format="jplace" label="Placements"/>
21 </inputs>
22 <outputs>
23 <data name="reduped_seqs" format="jplace" label="Reduped placements"/>
24 <data name="class_db" format="sqlite3" label="Placement database"/>
25 </outputs>
26 <configfiles>
27 <configfile name="config">
28 DEDUP_INFO="${dedup_info}"
29 REFPKG="${refpkg.extra_files_path}"
30 NBC_SEQS="${nbc_seqs}"
31 PLACED_SEQS="${placed_seqs}"
32
33 REDUPED_SEQS="${reduped_seqs}"
34 CLASS_DB="${class_db}"
35 </configfile>
36 </configfiles>
37 <!-- The contents of the help tag is parsed as reStructuredText. Please see
38 help-template.rst for examples of commonly-used sections in other Galaxy
39 tools. -->
40 <help>
41
42 .. class:: infomark
43
44 **What it does**
45
46 This tool outputs the classifications made by ``pplacer`` to a database for use
47 in taxonomic classification.
48
49 </help>
50 </tool>