Mercurial > repos > abaizan > kodoja

comparison kodoja_search.xml @ 1:4554fcd4ef6d draft

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v0.0.6
author peterjc
date Wed, 05 Sep 2018 10:44:57 -0400
parents 18fe33eb7775
children ee917702dbd8
comparison
equal deleted inserted replaced
0:18fe33eb7775 1:4554fcd4ef6d
1 <tool id="kodoja_search" name="Kodoja database search" version="0.0.0"> 1 <tool id="kodoja_search" name="Kodoja database search" version="0.0.6">
2 <description>identify viruses from plant RNA sequencing data</description> 2 <description>identify viruses from plant RNA sequencing data</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.0.3">kodoja</requirement> 4 <requirement type="package" version="0.0.6">kodoja</requirement>
5 </requirements> 5 </requirements>
6 <version_command>kodoja_search.py --version</version_command> 6 <version_command>kodoja_search.py --version</version_command>
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 kodoja_search.py 8 kodoja_search.py
9 9
51 <options from_data_table="kaiju_databases"> 51 <options from_data_table="kaiju_databases">
52 <validator message="No Kaiju database is available" type="no_options" /> 52 <validator message="No Kaiju database is available" type="no_options" />
53 </options> 53 </options>
54 </param> 54 </param>
55 <conditional name="single_paired"> 55 <conditional name="single_paired">
56 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> 56 <param name="single_paired_selector" type="select" label="Single or paired reads">
57 <!-- TODO? 57 <!-- TODO?
58 <option value="collection">Collection</option> 58 <option value="collection">Collection</option>
59 --> 59 -->
60 <option value="yes">Paired</option> 60 <option value="yes">Paired</option>
61 <option selected="True" value="no">Single</option> 61 <option selected="True" value="no">Single</option>
100 <help><![CDATA[ 100 <help><![CDATA[
101 Kodoja is a tool intended to identify viral sequences in a 101 Kodoja is a tool intended to identify viral sequences in a
102 FASTQ/FASTA sequencing run by matching them against both 102 FASTQ/FASTA sequencing run by matching them against both
103 Kraken and Kaiju databases. 103 Kraken and Kaiju databases.
104 104
105 The main output is a five column tab-separated table as follows 105 The main output is a tab-separated table as follows (tabular format in Galaxy)
106 (tabular format in Galaxy): 106 with the following columns:
107 107
108 1. Species name 108 1. Species name
109 2. Species NCBI taxonomy identifier (TaxID) 109 2. Species NCBI taxonomy identifier (TaxID)
110 3. Number of reads assigned by *either* Kraken or Kaiju to this species 110 3. Number of reads assigned by *either* Kraken or Kaiju to this species
111 4. Number of Reads assigned by *both* Kraken and Kaiju to this species 111 4. Number of Reads assigned by *both* Kraken and Kaiju to this species