comparison gottcha.xml @ 1:87efdde6105f draft

planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48-dirty

0:2569a83977f5

<tool id="gottcha" name="GOTTCHA" version="0.0.1">

    <description>Read-based metagenome characterization</description>

    <!-- ***************************************************************** -->

    <requirements>
        <requirement type="package" version="1.0b-564cf3b">gottcha</requirement>
    </requirements>

    <!-- ***************************************************************** -->

    <version_command>gottcha.pl -h | perl -wnE'print "$1\n" for /VERSION: (\S+)/g'</version_command>

    <!-- ***************************************************************** -->

    <help>
    <![CDATA[

.. class:: infomark

Description
--------------------

Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) is an
annotation-independent and signature-based metagenomic taxonomic profiling
tool that has significantly smaller FDR than other profiling tools. This Perl
script is a wrapper to run the GOTTCHA profiling tool with pre-computed
signature databases. The procedure includes 3 major steps: split-trimming the
input data, mapping reads to a GOTTCHA database using BWA, profiling/filtering
the result.

Options
--------------------
::

    --relAbu|r   <STRING>  The field will be used to calculate relative
                           abundance. You can specify one of the following
                           fields: "LINEAR_LENGTH", "TOTAL_BP_MAPPED",

    --minLen     <INT>     Minimum unique length to be considered valid in
                           abundance calculation [default: 100]
    --minHits    <INT>     Minimum number of hits to be considered valid in 
                           abundance calculation [10]

Interpreting Results
--------------------

GOTTCHA reports profiling results in a neat summary table
by default. The tsv file will list the organism(s) at all taxonomic
levels from STRAIN to PHYLUM, their linear length, total bases mapped,
linear depth of coverage, and the normalized linear depth of coverage. The

1:87efdde6105f

<tool id="gottcha" name="GOTTCHA" version="0.001">

    <description>Read-based metagenome characterization</description>

    <!-- ***************************************************************** -->

    <requirements>
        <requirement type="package" version="1.0b-564cf3b">gottcha</requirement>
        <requirement type="package" version="0.7.12">bwa</requirement>
    </requirements>

    <!-- ***************************************************************** -->

    <version_command>gottcha.pl -h | perl -wnE'print "$1\n" for /VERSION: (\S+)/g'</version_command>

    <!-- ***************************************************************** -->

    <help>
    <![CDATA[

**Description**

Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) is an
annotation-independent and signature-based metagenomic taxonomic profiling
tool that has significantly smaller FDR than other profiling tools. This Perl
script is a wrapper to run the GOTTCHA profiling tool with pre-computed
signature databases. The procedure includes 3 major steps: split-trimming the
input data, mapping reads to a GOTTCHA database using BWA, profiling/filtering
the result.

**Options**
::

    --relAbu|r   <STRING>  The field will be used to calculate relative
                           abundance. You can specify one of the following
                           fields: "LINEAR_LENGTH", "TOTAL_BP_MAPPED",

    --minLen     <INT>     Minimum unique length to be considered valid in
                           abundance calculation [default: 100]
    --minHits    <INT>     Minimum number of hits to be considered valid in 
                           abundance calculation [10]

**Interpreting Results**

GOTTCHA reports profiling results in a neat summary table
by default. The tsv file will list the organism(s) at all taxonomic
levels from STRAIN to PHYLUM, their linear length, total bases mapped,
linear depth of coverage, and the normalized linear depth of coverage. The