Mercurial > repos > jasper > cluster_picker
comparison cluster_picker-661b74ba4cc8/cluster-picker.xml @ 0:597bff809239 draft default tip
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| author | jasper |
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| date | Thu, 13 Apr 2017 16:23:47 -0400 |
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| -1:000000000000 | 0:597bff809239 |
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| 1 <tool id="cluster-pick" name="Cluster Picker" version="1.2.3"> | |
| 2 <description>cluster picker</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="1.2.3">cluster-picker</requirement> | |
| 5 </requirements> | |
| 6 <command> <![CDATA[ln -s '$sequence_file' seq.dat && | |
| 7 ln -s '$tree_file' tree.dat && | |
| 8 cluster-picker seq.dat tree.dat $init_threshold $main_threshold $dis_threshold $size $genetic_distance | |
| 9 ]]> </command> | |
| 10 <inputs> | |
| 11 <param format="fasta" name="sequence_file" type="data" label="align" | |
| 12 help="Please enter fasta format sequences file name to process"/> | |
| 13 <param format="nhx" name="tree_file" type="data" label="tree" | |
| 14 help="Please enter newick format tree, with branch lengths and node support"/> | |
| 15 <param name="init_threshold" type="float" value="0.9" optional="true" | |
| 16 help="Please enter initial support threshold for these initial subtrees" label="initial threshold"> | |
| 17 </param> | |
| 18 <param name="main_threshold" type="float" value="0.9" optional="true" | |
| 19 help="Please enter main support threshold for clusters" label="main threshold"> | |
| 20 </param> | |
| 21 <param name="dis_threshold" type="float" value="0.045" optional="true" | |
| 22 help="Please enter genetic distance threshold for clusters in %" label="distance threshold"> | |
| 23 </param> | |
| 24 <param name="size" type="integer" value="10" optional="true" | |
| 25 help="To output all cluster names for clusters of size >= X enter X" label="size"> | |
| 26 </param> | |
| 27 <param name="genetic_distance" type="select" label="genetic distance" | |
| 28 help="Please enter scoring type for genetic distance\n | |
| 29 gap = disregard sites with -, ~, or n\n | |
| 30 abs = count absolute character differences\n | |
| 31 valid = only count differences for sites with nucleotides: a, c, t, g in both sequences\n | |
| 32 ambiguity = disregard sites with -, ~, or n and do not count ambiguities as differences (e.g. a vs r is not a difference)"> | |
| 33 <option value="gap">gap</option> | |
| 34 <option value="abs">abs</option> | |
| 35 <option value="valid">valid</option> | |
| 36 <option value="ambiguity">ambiguity</option> | |
| 37 </param> | |
| 38 </inputs> | |
| 39 <outputs> | |
| 40 <data name='fig' format="figTree" from_work_dir="tree_clusterPicks.nwk.figTree"/> | |
| 41 <data name='tr' format="nhx" from_work_dir="tree_clusterPicks.nwk"/> | |
| 42 <data name='log' format="txt" from_work_dir="tree_clusterPicks_log.txt"/> | |
| 43 <data name='seq' format="fasta" from_work_dir="seq.dat_tree_clusterPicks.fasta"/> | |
| 44 </outputs> | |
| 45 | |
| 46 <tests> | |
| 47 <test> | |
| 48 <param name="sequence_file" value="dummy.fasta" /> | |
| 49 <param name="tree_file" value="dummy.nhx" /> | |
| 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> | |
| 58 </tests> | |
| 59 | |
| 60 <help> | |
| 61 Cluster identification strategies differ between studies and as a consequence cluster definitions vary. | |
| 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> | |
| 73 </tool> |