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comparison preprocessing.xml @ 2:ce6db18f5fd3 draft

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author bcclaywell
date Thu, 26 Feb 2015 19:31:20 -0500
parents d4690e65afcd
children 221a97bf686d
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1:c8cc6529038c 2:ce6db18f5fd3
1 <tool id="PHYLO_preprocessing" name="Preprocess sequences" version="2.0.0">
2 <description>in preparation for phylogenetic placement</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 preprocessing-wrapper.sh ${config}
12 </command>
13 <stdio>
14 <expand macro="basic_errors"/>
15 </stdio>
16 <inputs>
17 <param name="refpkg" type="data" format="refpkg" label="Reference package"/>
18 <param name="input_seqs" type="data" format="fasta" label="Input sequences"/>
19 <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/>
20 </inputs>
21 <outputs>
22 <data name="dedup_seqs" format="fasta" label="Deduplicated sequences"/>
23 <data name="dedup_info" format="csv" label="Deduplication info"/>
24 <data name="aligned_seqs" format="fasta" label="Aligned sequences"/>
25 <data name="aligned_scores" format="txt" label="Alignment scores"/>
26 </outputs>
27 <configfiles>
28 <configfile name="config">
29 REFPKG="${refpkg.extra_files_path}"
30 INPUT_SEQS="${input_seqs}"
31 SPLIT_MAP="${split_map}"
32
33 DEDUP_SEQS="${dedup_seqs}"
34 DEDUP_INFO="${dedup_info}"
35 ALIGNED_SEQS="${aligned_seqs}"
36 ALIGNED_SCORES="${aligned_scores}"
37 </configfile>
38 </configfiles>
39 <!-- The contents of the help tag is parsed as reStructuredText. Please see
40 help-template.rst for examples of commonly-used sections in other Galaxy
41 tools. -->
42 <help>
43
44 .. class:: infomark
45
46 **What it does**
47
48 This tool aligns query sequences with the reference sequences used to make the
49 reference tree contained in the reference package and then merges the query and
50 reference sequences.
51
52 </help>
53 </tool>