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comparison kodoja_search.xml @ 2:ee917702dbd8 draft

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v0.0.7, support GALAXY_SLOTS etc
author peterjc
date Mon, 10 Sep 2018 09:16:13 -0400
parents 4554fcd4ef6d
children d4111d1de76f
comparison
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1:4554fcd4ef6d 2:ee917702dbd8
1 <tool id="kodoja_search" name="Kodoja database search" version="0.0.6"> 1 <tool id="kodoja_search" name="Kodoja database search" version="0.0.7">
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="0.0.6">kodoja</requirement> 4 <requirement type="package" version="0.0.7">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 -t="\${GALAXY_SLOTS:-4}"
10 --kraken_db '${kraken_db.fields.path}' 10 --kraken_db '${kraken_db.fields.path}'
11 --kaiju_db '${kaiju_db.fields.path}' 11 --kaiju_db '${kaiju_db.fields.path}'
12 12
13 #if $single_paired.single_paired_selector == 'yes' 13 #if $single_paired.single_paired_selector == 'yes'
14 #if $forward_input.is_of_type( 'fastq' ): 14 #if $forward_input.is_of_type( 'fastq' ):
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
112 5. Genus name 112 5. Genus name
113 6. Number of reads assigned by *either* Kraken or Kaiju to this genus 113 6. Number of reads assigned by *either* Kraken or Kaiju to this genus
114 7. Number of reads assigned by *both* Kraken and Kaiju to this genus 114 7. Number of reads assigned by *both* Kraken and Kaiju to this genus
115 115
116 The counts in columns 6 and 7 are for reads assigned to that genus, but not
117 to any species within it.
118
116 For example, 119 For example,
117 120
118 ================================== ============= ================= ============================= ========== =============== =========================== 121 ================================== ============= ================= ============================= ========== =============== ===========================
119 Species Species TaxID Species sequences Species sequences (stringent) Genus Genus sequences Genus sequences (stringent) 122 Species Species TaxID Species sequences Species sequences (stringent) Genus Genus sequences Genus sequences (stringent)
120 ---------------------------------- ------------- ----------------- ----------------------------- ---------- --------------- --------------------------- 123 ---------------------------------- ------------- ----------------- ----------------------------- ---------- --------------- ---------------------------
121 Cassava brown streak virus 137758 45 45 Ipomovirus 124 Cassava brown streak virus 137758 45 45 Ipomovirus 0 0
122 Ugandan cassava brown streak virus 946046 28 28 Ipomovirus 125 Ugandan cassava brown streak virus 946046 28 28 Ipomovirus 0 0
123 Tobacco etch virus 12227 21 19 Potyvirus 126 Tobacco etch virus 12227 21 19 Potyvirus 0 0
124 ================================== ============= ================= ============================= ========== =============== =========================== 127 ================================== ============= ================= ============================= ========== =============== ===========================
125 128
126 This is the command line tool's help:: 129 The command line tool offers additional options not currently exposed
130 in Galaxy, including::
127 131
128 usage: kodoja_search.py [-h] [--version] -o OUTPUT_DIR -d1 KRAKEN_DB -d2
129 KAIJU_DB -r1 READ1 [-r2 READ2] [-f DATA_FORMAT]
130 [-t THREADS] [-s] [-m TRIM_MINLEN] [-a TRIM_ADAPT]
131 [-q KRAKEN_QUICK] [-p] [-c KAIJU_SCORE]
132 [-l KAIJU_MINLEN] [-i KAIJU_MISMATCH]
133
134 Kodoja
135
136 optional arguments:
137 -h, --help show this help message and exit
138 --version show program's version number and exit
139 -o OUTPUT_DIR, --output_dir OUTPUT_DIR
140 Output directory path, required
141 -d1 KRAKEN_DB, --kraken_db KRAKEN_DB
142 Kraken database path, required
143 -d2 KAIJU_DB, --kaiju_db KAIJU_DB
144 Kaiju database path, required
145 -r1 READ1, --read1 READ1
146 Read 1 file path, required
147 -r2 READ2, --read2 READ2
148 Read 2 file path
149 -f DATA_FORMAT, --data_format DATA_FORMAT
150 Sequence data format
151 -t THREADS, --threads THREADS
152 Number of threads 132 Number of threads
153 -s, --host_subset Subset host sequences before Kaiju 133 -s, --host_subset Subset host sequences before Kaiju
154 -m TRIM_MINLEN, --trim_minlen TRIM_MINLEN 134 -m TRIM_MINLEN, --trim_minlen TRIM_MINLEN
155 Trimmomatic minimum length 135 Trimmomatic minimum length
156 -a TRIM_ADAPT, --trim_adapt TRIM_ADAPT 136 -a TRIM_ADAPT, --trim_adapt TRIM_ADAPT
163 -l KAIJU_MINLEN, --kaiju_minlen KAIJU_MINLEN 143 -l KAIJU_MINLEN, --kaiju_minlen KAIJU_MINLEN
164 Kaju minimum length 144 Kaju minimum length
165 -i KAIJU_MISMATCH, --kaiju_mismatch KAIJU_MISMATCH 145 -i KAIJU_MISMATCH, --kaiju_mismatch KAIJU_MISMATCH
166 Kaju allowed mismatches 146 Kaju allowed mismatches
167 147
148
149 For more information, please see the Kodoja manual
150 https://github.com/abaizan/kodoja/wiki/Kodoja-Manual
168 ]]></help> 151 ]]></help>
169 <citations> 152 <citations>
170 <citation type="bibtex"> 153 <citation type="bibtex">
171 @misc{githubkodoja, 154 @misc{githubkodoja,
172 author = {Baizan Edge, Amanda}, 155 author = {Baizan Edge, Amanda},