Mercurial > repos > boris > phylorelatives
annotate phylorelatives.xml @ 41:9453ba52f46b draft
tool now uses multiple selection for input fasta files
| author | boris |
|---|---|
| date | Fri, 19 Jul 2013 17:46:03 -0400 |
| parents | c340422b78b1 |
| children |
| rev | line source |
|---|---|
| 9 | 1 <tool id="phylorelatives" name="Phylorelatives" version="0.0.1"> |
| 2 <description>Relatedness of minor alelle sequences in NJ tree</description> | |
| 3 <requirements> | |
| 4 <requirement type="package" version="2.15.0">R</requirement> | |
| 5 <requirement type="package" version="2.2.6">rpy2</requirement> | |
| 6 <requirement type="package" version="3.12.0">dendropy</requirement> | |
| 7 <requirement type="package" version="3.0-8">ape</requirement> | |
| 8 </requirements> | |
| 9 <command interpreter="python">phylorelatives.py | |
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9453ba52f46b
tool now uses multiple selection for input fasta files
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10 #for $sequence in ( $sequences ): |
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tool now uses multiple selection for input fasta files
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11 -i "${sequence}" |
| 9 | 12 #end for |
| 13 -m "${multifasta}" | |
| 14 -b "$iterations" | |
| 15 $pairwise | |
| 34 | 16 $major_only |
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17 #if str($root.root_selector)=="add_root": |
| 9 | 18 -r "${root.root_fa}" |
| 19 #end if | |
| 20 --relatives-out "$siblings" | |
| 21 --newick-out "$newick" | |
| 22 --trees-out "$plot" | |
| 23 </command> | |
| 24 <inputs> | |
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tool now uses multiple selection for input fasta files
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25 <param format="fasta" name="sequences" type="data" label="FASTA file" multiple="TRUE" help="Minor allele sequences must be labeled "_minor" or "_test" e.g. ">sample1_minor""> |
| 9 | 26 </param> |
| 27 <conditional name="root"> | |
| 28 <param name="root_selector" type="select" label=" Root sequence"> | |
| 29 <option value="unrooted" selected="True"></option> | |
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tool now uses multiple selection for input fasta files
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30 <option value="add_root"></option> |
| 9 | 31 </param> |
| 32 <when value="unrooted"> | |
| 33 </when> | |
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34 <when value="add_root"> |
| 9 | 35 <param name="root_fa" format="fasta" type="data" label="Root tree using" help="Must have the same length as input sequences"/> |
| 36 </when> | |
| 37 </conditional> | |
| 38 <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to "Complete deletion""/> | |
| 34 | 39 <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/> |
| 38 | 40 <param name="major_only" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Major-alleles-only mode" help="All sequences will be treated as major allele sequences. Useful to generate background tree"/> |
| 9 | 41 </inputs> |
| 42 <outputs> | |
| 34 | 43 <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta used" /> |
| 44 <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives list"/> | |
| 38 | 45 <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick string"/> |
| 36 | 46 <data format="png" name="plot" label="${tool.name} on ${on_string}: tree plot"/> |
| 9 | 47 </outputs> |
| 48 <tests> | |
| 49 <test> | |
| 50 <param name="iterations" value="0"/> | |
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tool now uses multiple selection for input fasta files
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51 <param name="sequences" value="test.fa"/> |
| 9 | 52 <output name="siblings" file="test.fa-siblings.tab"/> |
| 53 </test> | |
| 54 </tests> | |
| 55 | |
| 56 <help> | |
| 57 | |
| 58 | |
| 59 | |
| 38 | 60 The major and minor allele sequences of a sample are expected to cluster together in a phylogenetic tree. |
| 61 Deviation from expectation suggests potential contamination coming from the closest unrelated samples. | |
| 34 | 62 |
| 9 | 63 ----- |
| 64 | |
| 65 .. class:: infomark | |
| 66 | |
| 67 **What it does** | |
| 68 | |
| 69 Constructs relatedness of a set of sequences based on the pairwise proportion of different sites. | |
| 70 One or more test sequences are accepted as long as their name include the strict suffix "_minor" or "_test" (i.e. >seq1_minor). | |
| 38 | 71 It returns the FASTA multiple alignment used, and reports a table with the closest major allele relatives, the tree plot and newick string of the tree. |
| 9 | 72 |
| 73 ----- | |
| 74 | |
| 75 .. class:: warningmark | |
| 76 | |
| 77 **Note** | |
| 78 | |
| 79 This tools DOES NOT align the sequences. | |
| 38 | 80 Consequently, same length homologous sequences are required as input to fabricate a FASTA multiple alignment by concatenation of individual FASTA files. |
| 9 | 81 |
| 82 ----- | |
| 83 | |
| 84 .. class:: infomark | |
| 85 | |
| 86 **About formats** | |
| 87 | |
| 32 | 88 *FASTA multiple alignment* |
| 9 | 89 |
| 32 | 90 See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format |
| 9 | 91 |
| 38 | 92 *Newick* |
| 93 | |
| 94 http://www.megasoftware.net/WebHelp/glossary/rh_newick_format.htm | |
| 95 | |
| 9 | 96 ----- |
| 97 | |
| 98 **Example** | |
| 99 | |
| 38 | 100 - For the multiple alignment composed of the following FASTA files:: |
| 101 | |
| 102 >sample1_major | |
| 103 >sample1_minor | |
| 104 >sample2_major | |
| 105 >sample3_major | |
| 106 >sample4_major | |
| 9 | 107 |
| 108 | |
| 38 | 109 - running this tool with *root = RSRS.fasta*, and default parameters will return four datasets:: |
| 110 | |
| 111 1. multiple alignment file used for running the tool | |
| 112 2. relatives of sample1_minor | |
| 113 3. NJ tree newick string (rooted on RSRS) | |
| 114 4. NJ tree png plot (rooted on RSRS) | |
| 32 | 115 |
| 116 ----- | |
| 117 | |
| 118 **Citation** | |
| 119 | |
| 120 If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.* | |
| 121 (boris-at-bx.psu.edu) | |
| 122 | |
| 9 | 123 </help> |
| 124 | |
| 125 </tool> |