Mercurial > repos > bcclaywell > microbiome_pplacer_suite
comparison preprocessing.xml @ 3:221a97bf686d draft
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author | bcclaywell |
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date | Wed, 25 Mar 2015 16:39:10 -0400 |
parents | d4690e65afcd |
children | 3c50a937d7c1 |
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2:ce6db18f5fd3 | 3:221a97bf686d |
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1 <tool id="PHYLO_preprocessing" name="Preprocess sequences" version="2.0.0"> | 1 <tool id="PHYLO_preprocessing" name="Deduplicate sequences" version="3.0.0"> |
2 <description>in preparation for phylogenetic placement</description> | 2 <description>in preparation for alignment and placement</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package">yapp_env</requirement> | 4 <requirement type="package">yapp_env</requirement> |
5 </requirements> | 5 </requirements> |
6 <macros> | 6 <macros> |
7 <import>macros.xml</import> | 7 <import>macros.xml</import> |
12 </command> | 12 </command> |
13 <stdio> | 13 <stdio> |
14 <expand macro="basic_errors"/> | 14 <expand macro="basic_errors"/> |
15 </stdio> | 15 </stdio> |
16 <inputs> | 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"/> | 17 <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"/> | 18 <param name="split_map" type="data" format="csv" label="Read-to-specimen map"/> |
20 </inputs> | 19 </inputs> |
21 <outputs> | 20 <outputs> |
22 <data name="dedup_seqs" format="fasta" label="Deduplicated sequences"/> | 21 <data name="dedup_seqs" format="fasta" label="Deduplicated sequences"/> |
23 <data name="dedup_info" format="csv" label="Deduplication info"/> | 22 <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> | 23 </outputs> |
27 <configfiles> | 24 <configfiles> |
28 <configfile name="config"> | 25 <configfile name="config"> |
29 REFPKG="${refpkg.extra_files_path}" | |
30 INPUT_SEQS="${input_seqs}" | 26 INPUT_SEQS="${input_seqs}" |
31 SPLIT_MAP="${split_map}" | 27 SPLIT_MAP="${split_map}" |
32 | 28 |
33 DEDUP_SEQS="${dedup_seqs}" | 29 DEDUP_SEQS="${dedup_seqs}" |
34 DEDUP_INFO="${dedup_info}" | 30 DEDUP_INFO="${dedup_info}" |
35 ALIGNED_SEQS="${aligned_seqs}" | |
36 ALIGNED_SCORES="${aligned_scores}" | |
37 </configfile> | 31 </configfile> |
38 </configfiles> | 32 </configfiles> |
39 <!-- The contents of the help tag is parsed as reStructuredText. Please see | 33 <!-- 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 | 34 help-template.rst for examples of commonly-used sections in other Galaxy |
41 tools. --> | 35 tools. --> |
43 | 37 |
44 .. class:: infomark | 38 .. class:: infomark |
45 | 39 |
46 **What it does** | 40 **What it does** |
47 | 41 |
48 This tool aligns query sequences with the reference sequences used to make the | 42 This tool deduplicates input sequences in preparation for alignment and placement. |
49 reference tree contained in the reference package and then merges the query and | |
50 reference sequences. | |
51 | 43 |
52 </help> | 44 </help> |
53 </tool> | 45 </tool> |