Mercurial > repos > devteam > kraken_filter
changeset 3:5bee9adae474 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_filter/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd
author | iuc |
---|---|
date | Mon, 07 Aug 2017 17:29:19 -0400 |
parents | fe94f318048c |
children | 3d6570bffdb1 |
files | kraken-filter.xml macros.xml tool_dependencies.xml |
diffstat | 3 files changed, 23 insertions(+), 29 deletions(-) [+] |
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--- a/kraken-filter.xml Wed Mar 23 11:00:18 2016 -0400 +++ b/kraken-filter.xml Mon Aug 07 17:29:19 2017 -0400 @@ -1,22 +1,24 @@ -<tool id="kraken-filter" name="Kraken-filter" version="1.2.1"> - <description> - filter classification by confidence score - </description> +<tool id="kraken-filter" name="Kraken-filter" version="@WRAPPER_VERSION@"> + <description>filter classification by confidence score</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> - <expand macro="stdio" /> <expand macro="version_command" /> - <command> - <![CDATA[ + <command detect_errors="exit_code"><![CDATA[ @SET_DATABASE_PATH@ && - kraken-filter @INPUT_DATABASE@ --threshold $threshold "${input}" > "$filtered_output" - ]]> - </command> + + kraken-filter + @INPUT_DATABASE@ + --threshold $threshold + '${input}' + > '$filtered_output' + ]]></command> <inputs> - <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/> - <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" help="--threshold; A number between 0 and 1; default=0"/> + <param name="input" type="data" format="tabular" label="Kraken output" help="Select taxonomy classification produced by kraken"/> + <param argument="--threshold" type="float" value="0" min="0" max="1" + label="Confidence threshold" help="A floating point number between 0 and 1; default=0"/> + <expand macro="input_database" /> </inputs> <outputs> @@ -27,7 +29,8 @@ <param name="input" value="kraken_filter_test1.tab"/> <param name="threshold" value="0"/> <param name="kraken_database" value="test_db"/> - <output name="output" file="kraken_filter_test1_output.tab" ftype="tabular"/> + + <output name="filtered_output" file="kraken_filter_test1_output.tab" ftype="tabular"/> </test> </tests> @@ -46,7 +49,7 @@ A sequence label's score is a fraction C/Q, where C is the number of k-mers mapped to LCA values in the clade rooted at the label, and Q is the number of k-mers in the sequence that lack an ambiguous nucleotide (i.e., they were queried against the database). Consider the example of the LCA mappings in Kraken's output:: - 562:13 561:4 A:31 0:1 562:3 + 562:13 561:4 A:31 0:1 562:3 would indicate that::
--- a/macros.xml Wed Mar 23 11:00:18 2016 -0400 +++ b/macros.xml Mon Aug 07 17:29:19 2017 -0400 @@ -1,23 +1,20 @@ <?xml version="1.0"?> <macros> + <token name="@WRAPPER_VERSION@">1.2.3</token> <xml name="requirements"> <requirements> <requirement type="package" version="0.10.6_eaf8fb68">kraken</requirement> - <requirement type="package" version="0.10.6-eaf8fb68">kraken</requirement> </requirements> </xml> - <xml name="stdio"> - <stdio> - <exit_code description="Tool exception" level="fatal" range="1:" /> - </stdio> - </xml> <xml name="version_command"> - <version_command>export LC_ALL=C && kraken --version</version_command> + <version_command><![CDATA[ + export LC_ALL=C && kraken --version + ]]></version_command> </xml> <xml name="input_database"> <param label="Select a Kraken database" name="kraken_database" type="select"> <options from_data_table="kraken_databases"> - <validator message="No databases are available built-in" type="no_options" /> + <validator message="No Kraken database is available" type="no_options" /> </options> </param> </xml> @@ -28,4 +25,4 @@ </xml> <token name="@INPUT_DATABASE@">--db ${kraken_database.fields.name}</token> <token name="@SET_DATABASE_PATH@">export KRAKEN_DB_PATH="${kraken_database.fields.path}"</token> -</macros> \ No newline at end of file +</macros>
--- a/tool_dependencies.xml Wed Mar 23 11:00:18 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="kraken" version="0.10.6-eaf8fb68"> - <repository changeset_revision="0743afe4dcb8" name="package_kraken_0_10_6_eaf8fb68" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>