comparison kodoja_search.xml @ 2:ee917702dbd8 draft

v0.0.7, support GALAXY_SLOTS etc

1:4554fcd4ef6d

<tool id="kodoja_search" name="Kodoja database search" version="0.0.6">
    <description>identify viruses from plant RNA sequencing data</description>
    <requirements>
        <requirement type="package" version="0.0.6">kodoja</requirement>
    </requirements>
    <version_command>kodoja_search.py --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
kodoja_search.py

--kraken_db '${kraken_db.fields.path}'
--kaiju_db '${kaiju_db.fields.path}'

#if $single_paired.single_paired_selector == 'yes'
    #if $forward_input.is_of_type( 'fastq' ):

4. Number of Reads assigned by *both* Kraken and Kaiju to this species
5. Genus name
6. Number of reads assigned by *either* Kraken or Kaiju to this genus
7. Number of reads assigned by *both* Kraken and Kaiju to this genus

For example,

================================== ============= ================= ============================= ========== =============== ===========================
Species                            Species TaxID Species sequences Species sequences (stringent) Genus      Genus sequences Genus sequences (stringent)
---------------------------------- ------------- ----------------- ----------------------------- ---------- --------------- ---------------------------
Cassava brown streak virus                137758                45                            45 Ipomovirus
Ugandan cassava brown streak virus        946046                28                            28 Ipomovirus
Tobacco etch virus                         12227                21                            19 Potyvirus
================================== ============= ================= ============================= ========== =============== ===========================

This is the command line tool's help::

    usage: kodoja_search.py [-h] [--version] -o OUTPUT_DIR -d1 KRAKEN_DB -d2
    KAIJU_DB -r1 READ1 [-r2 READ2] [-f DATA_FORMAT]
    [-t THREADS] [-s] [-m TRIM_MINLEN] [-a TRIM_ADAPT]
    [-q KRAKEN_QUICK] [-p] [-c KAIJU_SCORE]
    [-l KAIJU_MINLEN] [-i KAIJU_MISMATCH]

    Kodoja

    optional arguments:
      -h, --help            show this help message and exit
      --version             show program's version number and exit
      -o OUTPUT_DIR, --output_dir OUTPUT_DIR
                            Output directory path, required
      -d1 KRAKEN_DB, --kraken_db KRAKEN_DB
                            Kraken database path, required
      -d2 KAIJU_DB, --kaiju_db KAIJU_DB
                            Kaiju database path, required
      -r1 READ1, --read1 READ1
                            Read 1 file path, required
      -r2 READ2, --read2 READ2
                            Read 2 file path
      -f DATA_FORMAT, --data_format DATA_FORMAT
                            Sequence data format
      -t THREADS, --threads THREADS
                            Number of threads
      -s, --host_subset     Subset host sequences before Kaiju
      -m TRIM_MINLEN, --trim_minlen TRIM_MINLEN
                            Trimmomatic minimum length
      -a TRIM_ADAPT, --trim_adapt TRIM_ADAPT

      -l KAIJU_MINLEN, --kaiju_minlen KAIJU_MINLEN
                            Kaju minimum length
      -i KAIJU_MISMATCH, --kaiju_mismatch KAIJU_MISMATCH
                            Kaju allowed mismatches

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubkodoja,
  author = {Baizan Edge, Amanda},

2:ee917702dbd8

<tool id="kodoja_search" name="Kodoja database search" version="0.0.7">
    <description>identify viruses from plant RNA sequencing data</description>
    <requirements>
        <requirement type="package" version="0.0.7">kodoja</requirement>
    </requirements>
    <version_command>kodoja_search.py --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
kodoja_search.py
-t="\${GALAXY_SLOTS:-4}"
--kraken_db '${kraken_db.fields.path}'
--kaiju_db '${kaiju_db.fields.path}'

#if $single_paired.single_paired_selector == 'yes'
    #if $forward_input.is_of_type( 'fastq' ):

4. Number of Reads assigned by *both* Kraken and Kaiju to this species
5. Genus name
6. Number of reads assigned by *either* Kraken or Kaiju to this genus
7. Number of reads assigned by *both* Kraken and Kaiju to this genus

The counts in columns 6 and 7 are for reads assigned to that genus, but not
to any species within it.

For example,

================================== ============= ================= ============================= ========== =============== ===========================
Species                            Species TaxID Species sequences Species sequences (stringent) Genus      Genus sequences Genus sequences (stringent)
---------------------------------- ------------- ----------------- ----------------------------- ---------- --------------- ---------------------------
Cassava brown streak virus                137758                45                            45 Ipomovirus               0                           0
Ugandan cassava brown streak virus        946046                28                            28 Ipomovirus               0                           0
Tobacco etch virus                         12227                21                            19 Potyvirus                0                           0
================================== ============= ================= ============================= ========== =============== ===========================

The command line tool offers additional options not currently exposed
in Galaxy, including::

                            Number of threads
      -s, --host_subset     Subset host sequences before Kaiju
      -m TRIM_MINLEN, --trim_minlen TRIM_MINLEN
                            Trimmomatic minimum length
      -a TRIM_ADAPT, --trim_adapt TRIM_ADAPT

      -l KAIJU_MINLEN, --kaiju_minlen KAIJU_MINLEN
                            Kaju minimum length
      -i KAIJU_MISMATCH, --kaiju_mismatch KAIJU_MISMATCH
                            Kaju allowed mismatches


For more information, please see the Kodoja manual
https://github.com/abaizan/kodoja/wiki/Kodoja-Manual
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubkodoja,
  author = {Baizan Edge, Amanda},