Mercurial > repos > xuebing > sharplabtool
comparison tools/taxonomy/find_diag_hits.xml @ 0:9071e359b9a3
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| author | xuebing |
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| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 <tool id="find_diag_hits" name="Find diagnostic hits" version="1.0.0"> | |
| 2 <description></description> | |
| 3 <requirements> | |
| 4 <requirement type="package">taxonomy</requirement> | |
| 5 </requirements> | |
| 6 <command interpreter="python">find_diag_hits.py $input1 $id_col $rank_list $out_format $out_file1</command> | |
| 7 <inputs> | |
| 8 <param format="taxonomy" name="input1" type="data" label="Find diagnostic hits in"/> | |
| 9 <param name="id_col" type="data_column" data_ref="input1" numerical="False" label="Select column with sequence id" /> | |
| 10 <param name="rank_list" type="select" display="checkboxes" multiple="true" label="select taxonomic ranks"> | |
| 11 <option value="superkingdom">Superkingdom</option> | |
| 12 <option value="kingdom">Kingdom</option> | |
| 13 <option value="subkingdom">Subkingdom</option> | |
| 14 <option value="superphylum">Superphylum</option> | |
| 15 <option value="phylum">Phylum</option> | |
| 16 <option value="subphylum">Subphylum</option> | |
| 17 <option value="superclass">Superclass</option> | |
| 18 <option value="class">Class</option> | |
| 19 <option value="subclass">Subclass</option> | |
| 20 <option value="superorder">Superorder</option> | |
| 21 <option value="order">Order</option> | |
| 22 <option value="suborder">Suborder</option> | |
| 23 <option value="superfamily">Superfamily</option> | |
| 24 <option value="family">Family</option> | |
| 25 <option value="subfamily">Subfamily</option> | |
| 26 <option value="tribe">Tribe</option> | |
| 27 <option value="subtribe">Subtribe</option> | |
| 28 <option value="genus">Genus</option> | |
| 29 <option value="subgenus">Subgenus</option> | |
| 30 <option selected="true" value="species">Species</option> | |
| 31 <option value="subspecies">Subspecies</option> | |
| 32 </param> | |
| 33 <param name="out_format" type="select" label="Select output format"> | |
| 34 <option value="reads">Diagnostic read list</option> | |
| 35 <option value="counts">Number of diagnostic reads per taxonomic rank</option> | |
| 36 </param> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data format="tabular" name="out_file1" /> | |
| 40 </outputs> | |
| 41 <tests> | |
| 42 <test> | |
| 43 <param name="input1" value="taxonomyGI.taxonomy" ftype="taxonomy"/> | |
| 44 <param name="id_col" value="1" /> | |
| 45 <param name="rank_list" value="order,genus" /> | |
| 46 <param name="out_format" value="counts" /> | |
| 47 <output name="out_file1" file="find_diag_hits.tabular" /> | |
| 48 </test> | |
| 49 </tests> | |
| 50 | |
| 51 | |
| 52 <help> | |
| 53 | |
| 54 **What it does** | |
| 55 | |
| 56 When performing metagenomic analyses it is often necessary to identify sequence reads corresponding to a particular taxonomic group, or, in other words, diagnostic of a particular taxonomic rank. This utility performs this analysis. It takes data generated by *Taxonomy manipulation->Fetch Taxonomic Ranks* as input and outputs either a list of sequence reads unique to a particular taxonomic rank, or a list of taxonomic ranks and the count of unique reads corresponding to each rank. | |
| 57 | |
| 58 ------ | |
| 59 | |
| 60 **Example** | |
| 61 | |
| 62 Suppose the *Taxonomy manipulation->Fetch Taxonomic Ranks* generated the following taxonomy representation:: | |
| 63 | |
| 64 read1 2 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Laurasiatheria n Ruminantia n Bovidae Bovinae n n Bos n Bos taurus n | |
| 65 read2 12585 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n | |
| 66 read1 58615 root Eukaryota Metazoa n n Arthropoda n Hexapoda Insecta Neoptera Amphiesmenoptera Lepidoptera Glossata Papilionoidea Nymphalidae Nymphalinae Melitaeini Phyciodina Anthanassa n Anthanassa otanes n | |
| 67 read3 56785 root Eukaryota Metazoa n n Chordata Craniata Gnathostomata Mammalia n Euarchontoglires Primates Haplorrhini Hominoidea Hominidae n n n Homo n Homo sapiens n | |
| 68 | |
| 69 Running this tool with the following parameters: | |
| 70 | |
| 71 * *Select column with sequence id* set to **c1** | |
| 72 * *Select taxonomic ranks* with **order**, and **genus** checked | |
| 73 * *Output format* set to **Diagnostic read list** | |
| 74 | |
| 75 will return:: | |
| 76 | |
| 77 read2 Primates order | |
| 78 read3 Primates order | |
| 79 read2 Homo genus | |
| 80 read3 Homo genus | |
| 81 | |
| 82 Changing *Output format* set to **Number of diagnostic reads per taxonomic rank** will produce:: | |
| 83 | |
| 84 Primates 2 order | |
| 85 Homo 2 genus | |
| 86 | |
| 87 .. class:: infomark | |
| 88 | |
| 89 Note that **read1** is omitted because it is non-unique: it hits Mammals and Insects at the same time. | |
| 90 | |
| 91 -------- | |
| 92 | |
| 93 .. class:: warningmark | |
| 94 | |
| 95 This tool omits "**n**" corresponding to ranks missing from NCBI taxonomy. In the above example *Home sapiens* contains the order name (Primates) while *Bos taurus* does not. | |
| 96 | |
| 97 | |
| 98 </help> | |
| 99 </tool> |