Mercurial > repos > bcclaywell > microbiome_pplacer_suite
comparison alignment.xml @ 3:221a97bf686d draft
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author | bcclaywell |
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date | Wed, 25 Mar 2015 16:39:10 -0400 |
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children | 3c50a937d7c1 |
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2:ce6db18f5fd3 | 3:221a97bf686d |
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1 <tool id="PHYLO_alignment" name="Align query sequences" version="1.0.0"> | |
2 <description>with sequences in a reference package</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 alignment-wrapper.sh ${config} | |
12 </command> | |
13 <stdio> | |
14 <expand macro="basic_errors"/> | |
15 </stdio> | |
16 <inputs> | |
17 <param name="refpkg" type="data" format="refpkg" label="Reference package"/> | |
18 <param name="input_seqs" type="data" format="fasta" label="Input sequences"/> | |
19 </inputs> | |
20 <outputs> | |
21 <data name="aligned_seqs" format="fasta" label="Aligned sequences"/> | |
22 <data name="aligned_scores" format="txt" label="Alignment scores"/> | |
23 </outputs> | |
24 <configfiles> | |
25 <configfile name="config"> | |
26 REFPKG="${refpkg.extra_files_path}" | |
27 INPUT_SEQS="${input_seqs}" | |
28 | |
29 ALIGNED_SEQS="${aligned_seqs}" | |
30 ALIGNED_SCORES="${aligned_scores}" | |
31 </configfile> | |
32 </configfiles> | |
33 <!-- The contents of the help tag is parsed as reStructuredText. Please see | |
34 help-template.rst for examples of commonly-used sections in other Galaxy | |
35 tools. --> | |
36 <help> | |
37 | |
38 .. class:: infomark | |
39 | |
40 **What it does** | |
41 | |
42 This tool aligns query sequences with the reference sequences used to make the | |
43 reference tree contained in the reference package and then merges the query and | |
44 reference sequences. | |
45 | |
46 </help> | |
47 </tool> |