| Previous changeset 1:4554fcd4ef6d (2018-09-05) Next changeset 3:d4111d1de76f (2018-09-14) |
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Commit message:
v0.0.7, support GALAXY_SLOTS etc |
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modified:
README.rst kodoja_search.xml test-data/virus_table_PE_fasta.tabular test-data/virus_table_PE_fastq.tabular test-data/virus_table_SE_fastq.tabular |
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| diff -r 4554fcd4ef6d -r ee917702dbd8 README.rst --- a/README.rst Wed Sep 05 10:44:57 2018 -0400 +++ b/README.rst Mon Sep 10 09:16:13 2018 -0400 |
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| @@ -77,6 +77,9 @@ v0.0.4 - Minor update to call ``kodoja_search.py`` v0.0.4. v0.0.6 - Minor update to call ``kodoja_search.py`` v0.0.6. - Document installing the Kodoja databases from Zenodo. +v0.0.7 - Minor update to call ``kodoja_search.py`` v0.0.6. + - Update help text, including zeros in columns 6 and 7. + - Support ``$GALAXY_SLOTS``, defaulting to using four threads. ======= ====================================================================== |
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| diff -r 4554fcd4ef6d -r ee917702dbd8 kodoja_search.xml --- a/kodoja_search.xml Wed Sep 05 10:44:57 2018 -0400 +++ b/kodoja_search.xml Mon Sep 10 09:16:13 2018 -0400 |
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| @@ -1,12 +1,12 @@ -<tool id="kodoja_search" name="Kodoja database search" version="0.0.6"> +<tool id="kodoja_search" name="Kodoja database search" version="0.0.7"> <description>identify viruses from plant RNA sequencing data</description> <requirements> - <requirement type="package" version="0.0.6">kodoja</requirement> + <requirement type="package" version="0.0.7">kodoja</requirement> </requirements> <version_command>kodoja_search.py --version</version_command> <command detect_errors="exit_code"><![CDATA[ kodoja_search.py - +-t="\${GALAXY_SLOTS:-4}" --kraken_db '${kraken_db.fields.path}' --kaiju_db '${kaiju_db.fields.path}' @@ -113,42 +113,22 @@ 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 -Ugandan cassava brown streak virus 946046 28 28 Ipomovirus -Tobacco etch virus 12227 21 19 Potyvirus +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 ================================== ============= ================= ============================= ========== =============== =========================== -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 +The command line tool offers additional options not currently exposed +in Galaxy, including:: - 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 @@ -165,6 +145,9 @@ -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"> |
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| diff -r 4554fcd4ef6d -r ee917702dbd8 test-data/virus_table_PE_fasta.tabular --- a/test-data/virus_table_PE_fasta.tabular Wed Sep 05 10:44:57 2018 -0400 +++ b/test-data/virus_table_PE_fasta.tabular Mon Sep 10 09:16:13 2018 -0400 |
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| @@ -1,4 +1,4 @@ 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 30 29 Ipomovirus -Tobacco etch virus 12227 25 23 Potyvirus +Cassava brown streak virus 137758 45 45 Ipomovirus 0 0 +Ugandan cassava brown streak virus 946046 30 29 Ipomovirus 0 0 +Tobacco etch virus 12227 25 23 Potyvirus 0 0 |
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| diff -r 4554fcd4ef6d -r ee917702dbd8 test-data/virus_table_PE_fastq.tabular --- a/test-data/virus_table_PE_fastq.tabular Wed Sep 05 10:44:57 2018 -0400 +++ b/test-data/virus_table_PE_fastq.tabular Mon Sep 10 09:16:13 2018 -0400 |
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| @@ -1,4 +1,4 @@ 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 +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 |
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| diff -r 4554fcd4ef6d -r ee917702dbd8 test-data/virus_table_SE_fastq.tabular --- a/test-data/virus_table_SE_fastq.tabular Wed Sep 05 10:44:57 2018 -0400 +++ b/test-data/virus_table_SE_fastq.tabular Mon Sep 10 09:16:13 2018 -0400 |
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| @@ -1,4 +1,4 @@ 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 29 29 Ipomovirus -Tobacco etch virus 12227 23 20 Potyvirus +Cassava brown streak virus 137758 45 45 Ipomovirus 0 0 +Ugandan cassava brown streak virus 946046 29 29 Ipomovirus 0 0 +Tobacco etch virus 12227 23 20 Potyvirus 0 0 |