Mercurial > repos > jasper > cluster_picker
comparison cluster-picker.xml @ 1:661b74ba4cc8 draft default tip
Uploaded
author | jasper |
---|---|
date | Fri, 03 Feb 2017 15:26:41 -0500 |
parents | 2040cda75d1f |
children |
comparison
equal
deleted
inserted
replaced
0:2040cda75d1f | 1:661b74ba4cc8 |
---|---|
1 <tool id="cluster-pick" name="Cluster Picker" version="1.2.3"> | 1 <tool id="cluster-pick" name="Cluster Picker" version="1.2.3"> |
2 <description>cluster picker</description> | 2 <description>cluster picker</description> |
3 <requirements> | 3 <requirements> |
4 <requirement type="package" version="1.2.3">cluster-picker</requirement> | 4 <requirement type="package" version="1.2.3">cluster-picker</requirement> |
5 </requirements> | 5 </requirements> |
6 <!-- <command> <![CDATA[cluster-picker sequence_file tree_file init_threshold main_threshold dis_threshold size genetic_distance]]> </command> --> | 6 <command> <![CDATA[ln -s '$sequence_file' seq.dat && |
7 <command> <![CDATA[cluster-picker]]> </command> | 7 ln -s '$tree_file' tree.dat && |
8 cluster-picker seq.dat tree.dat $init_threshold $main_threshold $dis_threshold $size $genetic_distance | |
9 ]]> </command> | |
8 <inputs> | 10 <inputs> |
9 <param format="fasta" name="sequence_file" type="data" label="align" | 11 <param format="fasta" name="sequence_file" type="data" label="align" |
10 help="Please enter fasta format sequences file name to process"/> | 12 help="Please enter fasta format sequences file name to process"/> |
11 <param format="nwk" name="tree_file" type="data" label="tree" | 13 <param format="nhx" name="tree_file" type="data" label="tree" |
12 help="Please enter newick format tree, with branch lengths and node support"/> | 14 help="Please enter newick format tree, with branch lengths and node support"/> |
13 <param name="init_threshold" type="float" value="0.9" optional="true" | 15 <param name="init_threshold" type="float" value="0.9" optional="true" |
14 help="Please enter initial support threshold for these initial subtrees" label="initial threshold"> | 16 help="Please enter initial support threshold for these initial subtrees" label="initial threshold"> |
15 </param> | 17 </param> |
16 <param name="main_threshold" type="float" value="0.9" optional="true" | 18 <param name="main_threshold" type="float" value="0.9" optional="true" |
17 help="Please enter main support threshold for clusters" label="main threshold"> | 19 help="Please enter main support threshold for clusters" label="main threshold"> |
18 </param> | 20 </param> |
19 <param name="dis_threshold" type="float" value="0.045" optional="true" | 21 <param name="dis_threshold" type="float" value="0.045" optional="true" |
20 help="Please enter genetic distance threshold for clusters in %" label="distance threshold"> | 22 help="Please enter genetic distance threshold for clusters in %" label="distance threshold"> |
21 </param> | 23 </param> |
22 <param name="size" type="float" value="10" optional="true" | 24 <param name="size" type="integer" value="10" optional="true" |
23 help="To output all cluster names for clusters of size >= X enter X" label="size"> | 25 help="To output all cluster names for clusters of size >= X enter X" label="size"> |
24 </param> | 26 </param> |
25 <param name="genetic_distance" type="select" label="genetic distance" | 27 <param name="genetic_distance" type="select" label="genetic distance" |
26 help="Please enter scoring type for genetic distance\n | 28 help="Please enter scoring type for genetic distance\n |
29 gap = disregard sites with -, ~, or n\n | |
27 abs = count absolute character differences\n | 30 abs = count absolute character differences\n |
28 gap = disregard sites with -, ~, or n\n | |
29 valid = only count differences for sites with nucleotides: a, c, t, g in both sequences\n | 31 valid = only count differences for sites with nucleotides: a, c, t, g in both sequences\n |
30 ambiguity = disregard sites with -, ~, or n and do not count ambiguities as differences (e.g. a vs r is not a difference)"> | 32 ambiguity = disregard sites with -, ~, or n and do not count ambiguities as differences (e.g. a vs r is not a difference)"> |
31 <option value="gap">gap</option> | 33 <option value="gap">gap</option> |
32 <option value="abs">abs</option> | 34 <option value="abs">abs</option> |
33 <option value="valid">valid</option> | 35 <option value="valid">valid</option> |
34 <option value="ambiguity">ambiguity</option> | 36 <option value="ambiguity">ambiguity</option> |
35 </param> | 37 </param> |
36 </inputs> | 38 </inputs> |
37 <outputs> | 39 <outputs> |
38 <data format="figTree"/> | 40 <data name='fig' format="figTree" from_work_dir="tree_clusterPicks.nwk.figTree"/> |
39 <data format="nhx"/> | 41 <data name='tr' format="nhx" from_work_dir="tree_clusterPicks.nwk"/> |
40 <data format="txt"/> | 42 <data name='log' format="txt" from_work_dir="tree_clusterPicks_log.txt"/> |
41 <data format="fasta"/> | 43 <data name='seq' format="fasta" from_work_dir="seq.dat_tree_clusterPicks.fasta"/> |
42 </outputs> | 44 </outputs> |
43 | 45 |
44 <tests> | 46 <tests> |
45 <test> | 47 <test> |
46 <param name="input" value="fa_gc_content_input.fa"/> | 48 <param name="sequence_file" value="dummy.fasta" /> |
47 <output name="out_file1" file="fa_gc_content_output.txt"/> | 49 <param name="tree_file" value="dummy.nhx" /> |
48 </test> | 50 <param name="init_threshold" value="0.9" /> |
51 <param name="main_threshold" value="0.9" /> | |
52 <param name="dis_threshold" value="0.045" /> | |
53 <param name="size" value="10" /> | |
54 <param name="genetic_distance" value="gap" /> | |
55 <param name="main_threshold" file="0.9" /> | |
56 <output name="fig" file="dummy.figTree" /> | |
57 </test> | |
49 </tests> | 58 </tests> |
50 | 59 |
51 <help> | 60 <help> |
52 Cluster identification strategies differ between studies and as a consequence cluster definitions vary. | 61 Cluster identification strategies differ between studies and as a consequence cluster definitions vary. |
53 </help> | 62 </help> |
63 <citations> | |
64 <citation type="bibtex">@ARTICLE{cluster-picker, | |
65 author = {Ragonnet-Cronin, Manon, et al;}, | |
66 title = {Automated analysis of phylogenetic clusters}, | |
67 journal = {BMC bioinformatics}, | |
68 year = {2013}, | |
69 volume = {14.1}, | |
70 pages = {317}} | |
71 </citation> | |
72 </citations> | |
54 </tool> | 73 </tool> |