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comparison kodoja_search.xml @ 3:d4111d1de76f draft default tip

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v0.0.8, expose kodoja_VRL.tsv output
author peterjc
date Fri, 14 Sep 2018 09:55:56 -0400
parents ee917702dbd8
children
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2:ee917702dbd8 3:d4111d1de76f
1 <tool id="kodoja_search" name="Kodoja database search" version="0.0.7"> 1 <tool id="kodoja_search" name="Kodoja database search" version="0.0.8">
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="0.0.7">kodoja</requirement> 4 <requirement type="package" version="0.0.8">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 ## This if statement is for backward compatibility as early versions of the Kraken
9 ## wrapper assumed the UI facing field name was also part of the directory path
10 if [ -d '${kraken_db.fields.path}/${kraken_db.fields.name}' ]; then export KRAKEN_DEFAULT_DB='${kraken_db.fields.path}/${kraken_db.fields.name}'; else export KRAKEN_DEFAULT_DB='${kraken_db.fields.path}'; fi &&
8 kodoja_search.py 11 kodoja_search.py
9 -t="\${GALAXY_SLOTS:-4}" 12 -t="\${GALAXY_SLOTS:-4}"
10 --kraken_db '${kraken_db.fields.path}' 13 --kraken_db "\$KRAKEN_DEFAULT_DB"
11 --kaiju_db '${kaiju_db.fields.path}' 14 --kaiju_db '${kaiju_db.fields.path}'
12 15
13 #if $single_paired.single_paired_selector == 'yes' 16 #if $single_paired.single_paired_selector == 'yes'
14 #if $forward_input.is_of_type( 'fastq' ): 17 #if $forward_input.is_of_type( 'fastq' ):
15 --data_format fastq 18 --data_format fastq
38 41
39 ## We'll capture predictably named output files from here: 42 ## We'll capture predictably named output files from here:
40 -o . 43 -o .
41 && 44 &&
42 mv ./virus_table.txt '$combined_table' 45 mv ./virus_table.txt '$combined_table'
46 #if $capture_reads_table:
47 &&
48 mv ./kodoja_VRL.txt '$reads_table'
49 #end if
43 ]]></command> 50 ]]></command>
44 <inputs> 51 <inputs>
45 <param label="Select a Kraken database" name="kraken_db" type="select"> 52 <param label="Select a Kraken database" name="kraken_db" type="select">
46 <options from_data_table="kraken_databases"> 53 <options from_data_table="kraken_databases">
47 <validator message="No Kraken database is available" type="no_options" /> 54 <validator message="No Kraken database is available" type="no_options" />
66 </when> 73 </when>
67 <when value="no"> 74 <when value="no">
68 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/> 75 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
69 </when> 76 </when>
70 </conditional> 77 </conditional>
78 <param name="capture_reads_table" type="boolean" value="false" label="Capture read assignment table" help="This table can be used to filter out reads matched to (individual) viruses"/>
71 </inputs> 79 </inputs>
72 <outputs> 80 <outputs>
73 <data name="combined_table" format="tabular" label="Kodoja species report for ${on_string}" /> 81 <data name="combined_table" format="tabular" label="Kodoja species report for ${on_string}" />
82 <data name="reads_table" format="tabular" label="Kodoja read assignment for ${on_string}">
83 <filter>capture_reads_table</filter>
84 </data>
74 </outputs> 85 </outputs>
75 <tests> 86 <tests>
76 <test> 87 <test>
77 <param name="kraken_db" value="kraken3viruses" /> 88 <param name="kraken_db" value="kraken3viruses" />
78 <param name="kaiju_db" value="kaiju3viruses" /> 89 <param name="kaiju_db" value="kaiju3viruses" />
85 <param name="kaiju_db" value="kaiju3viruses" /> 96 <param name="kaiju_db" value="kaiju3viruses" />
86 <param name="single_paired_selector" value="yes" /> 97 <param name="single_paired_selector" value="yes" />
87 <param name="forward_input" value="testData_1.fastq" ftype="fastq" /> 98 <param name="forward_input" value="testData_1.fastq" ftype="fastq" />
88 <param name="reverse_input" value="testData_2.fastq" ftype="fastq" /> 99 <param name="reverse_input" value="testData_2.fastq" ftype="fastq" />
89 <output name="combined_table" file="virus_table_PE_fastq.tabular" ftype="tabular" /> 100 <output name="combined_table" file="virus_table_PE_fastq.tabular" ftype="tabular" />
101 </test>
102 <test>
103 <param name="kraken_db" value="kraken3viruses" />
104 <param name="kaiju_db" value="kaiju3viruses" />
105 <param name="single_paired_selector" value="yes" />
106 <param name="forward_input" value="testData_1.fastq" ftype="fastq" />
107 <param name="reverse_input" value="testData_2.fastq" ftype="fastq" />
108 <param name="capture_reads_table" value="true" />
109 <output name="combined_table" file="virus_table_PE_fastq.tabular" ftype="tabular" />
110 <output name="reads_table" file="read_table_PE_fastq.tabular" ftype="tabular" />
90 </test> 111 </test>
91 <test> 112 <test>
92 <param name="kraken_db" value="kraken3viruses" /> 113 <param name="kraken_db" value="kraken3viruses" />
93 <param name="kaiju_db" value="kaiju3viruses" /> 114 <param name="kaiju_db" value="kaiju3viruses" />
94 <param name="single_paired_selector" value="yes" /> 115 <param name="single_paired_selector" value="yes" />
124 Cassava brown streak virus 137758 45 45 Ipomovirus 0 0 145 Cassava brown streak virus 137758 45 45 Ipomovirus 0 0
125 Ugandan cassava brown streak virus 946046 28 28 Ipomovirus 0 0 146 Ugandan cassava brown streak virus 946046 28 28 Ipomovirus 0 0
126 Tobacco etch virus 12227 21 19 Potyvirus 0 0 147 Tobacco etch virus 12227 21 19 Potyvirus 0 0
127 ================================== ============= ================= ============================= ========== =============== =========================== 148 ================================== ============= ================= ============================= ========== =============== ===========================
128 149
129 The command line tool offers additional options not currently exposed 150 The second most important output, which you can optionally capture
130 in Galaxy, including:: 151 for use within Galaxy, is a per-read table summarising matches found
152 with Kraken and/or Kaiju. The Kodoja Retrieve tool is not currently
153 available within Galaxy, but you can instead use this file directly
154 within Galaxy to filter out just the virus reads, or even reads
155 matched to a specific taxid. See for example ``seq_filter_by_id``
156 which is available via the Galaxy Tool Shed:
157
158 http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id
159 https://github.com/peterjc/pico_galaxy/tree/master/tools/seq_filter_by_id
160
161 The Kodoja Search command line tool offers additional options not
162 currently exposed in Galaxy, including::
131 163
132 Number of threads 164 Number of threads
133 -s, --host_subset Subset host sequences before Kaiju 165 -s, --host_subset Subset host sequences before Kaiju
134 -m TRIM_MINLEN, --trim_minlen TRIM_MINLEN 166 -m TRIM_MINLEN, --trim_minlen TRIM_MINLEN
135 Trimmomatic minimum length 167 Trimmomatic minimum length
143 -l KAIJU_MINLEN, --kaiju_minlen KAIJU_MINLEN 175 -l KAIJU_MINLEN, --kaiju_minlen KAIJU_MINLEN
144 Kaju minimum length 176 Kaju minimum length
145 -i KAIJU_MISMATCH, --kaiju_mismatch KAIJU_MISMATCH 177 -i KAIJU_MISMATCH, --kaiju_mismatch KAIJU_MISMATCH
146 Kaju allowed mismatches 178 Kaju allowed mismatches
147 179
148
149 For more information, please see the Kodoja manual 180 For more information, please see the Kodoja manual
150 https://github.com/abaizan/kodoja/wiki/Kodoja-Manual 181 https://github.com/abaizan/kodoja/wiki/Kodoja-Manual
151 ]]></help> 182 ]]></help>
152 <citations> 183 <citations>
153 <citation type="bibtex"> 184 <citation type="bibtex">