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comparison gottcha.xml @ 1:87efdde6105f draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48-dirty
author jdv
date Mon, 30 Jan 2017 19:26:53 -0500
parents 2569a83977f5
children dafd1d2cef8f
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0:2569a83977f5 1:87efdde6105f
1 <tool id="gottcha" name="GOTTCHA" version="0.0.1"> 1 <tool id="gottcha" name="GOTTCHA" version="0.001">
2 2
3 <description>Read-based metagenome characterization</description> 3 <description>Read-based metagenome characterization</description>
4 4
5 <!-- ***************************************************************** --> 5 <!-- ***************************************************************** -->
6 6
7 <requirements> 7 <requirements>
8 <requirement type="package" version="1.0b-564cf3b">gottcha</requirement> 8 <requirement type="package" version="1.0b-564cf3b">gottcha</requirement>
9 <requirement type="package" version="0.7.12">bwa</requirement>
9 </requirements> 10 </requirements>
10 11
11 <!-- ***************************************************************** --> 12 <!-- ***************************************************************** -->
12 13
13 <version_command>gottcha.pl -h | perl -wnE'print "$1\n" for /VERSION: (\S+)/g'</version_command> 14 <version_command>gottcha.pl -h | perl -wnE'print "$1\n" for /VERSION: (\S+)/g'</version_command>
118 <!-- ***************************************************************** --> 119 <!-- ***************************************************************** -->
119 120
120 <help> 121 <help>
121 <![CDATA[ 122 <![CDATA[
122 123
123 .. class:: infomark 124 **Description**
124
125 Description
126 --------------------
127 125
128 Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) is an 126 Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) is an
129 annotation-independent and signature-based metagenomic taxonomic profiling 127 annotation-independent and signature-based metagenomic taxonomic profiling
130 tool that has significantly smaller FDR than other profiling tools. This Perl 128 tool that has significantly smaller FDR than other profiling tools. This Perl
131 script is a wrapper to run the GOTTCHA profiling tool with pre-computed 129 script is a wrapper to run the GOTTCHA profiling tool with pre-computed
132 signature databases. The procedure includes 3 major steps: split-trimming the 130 signature databases. The procedure includes 3 major steps: split-trimming the
133 input data, mapping reads to a GOTTCHA database using BWA, profiling/filtering 131 input data, mapping reads to a GOTTCHA database using BWA, profiling/filtering
134 the result. 132 the result.
135 133
136 Options 134 **Options**
137 --------------------
138 :: 135 ::
139 136
140 --relAbu|r <STRING> The field will be used to calculate relative 137 --relAbu|r <STRING> The field will be used to calculate relative
141 abundance. You can specify one of the following 138 abundance. You can specify one of the following
142 fields: "LINEAR_LENGTH", "TOTAL_BP_MAPPED", 139 fields: "LINEAR_LENGTH", "TOTAL_BP_MAPPED",
175 --minLen <INT> Minimum unique length to be considered valid in 172 --minLen <INT> Minimum unique length to be considered valid in
176 abundance calculation [default: 100] 173 abundance calculation [default: 100]
177 --minHits <INT> Minimum number of hits to be considered valid in 174 --minHits <INT> Minimum number of hits to be considered valid in
178 abundance calculation [10] 175 abundance calculation [10]
179 176
180 Interpreting Results 177 **Interpreting Results**
181 --------------------
182 178
183 GOTTCHA reports profiling results in a neat summary table 179 GOTTCHA reports profiling results in a neat summary table
184 by default. The tsv file will list the organism(s) at all taxonomic 180 by default. The tsv file will list the organism(s) at all taxonomic
185 levels from STRAIN to PHYLUM, their linear length, total bases mapped, 181 levels from STRAIN to PHYLUM, their linear length, total bases mapped,
186 linear depth of coverage, and the normalized linear depth of coverage. The 182 linear depth of coverage, and the normalized linear depth of coverage. The