| Previous changeset 2:b9971bca4b01 (2016-03-23) Next changeset 4:9a5be5b1a5c9 (2019-12-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken_translate/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd |
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modified:
kraken-translate.xml macros.xml |
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removed:
tool_dependencies.xml |
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| diff -r b9971bca4b01 -r 9bdcba262627 kraken-translate.xml --- a/kraken-translate.xml Wed Mar 23 11:02:57 2016 -0400 +++ b/kraken-translate.xml Mon Aug 07 17:29:45 2017 -0400 |
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| @@ -1,26 +1,29 @@ -<tool id="kraken-translate" name="Kraken-translate" version="1.2.1"> - <description> - convert taxonomy IDs to names - </description> +<tool id="kraken-translate" name="Kraken-translate" version="@WRAPPER_VERSION@"> + <description>convert taxonomy IDs to names</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-translate @INPUT_DATABASE@ $mpa_format "${input}" > "${translated}" - ]]> - </command> + + kraken-translate + @INPUT_DATABASE@ + $mpa_format + '${input}' + > '${translated}' + ]]></command> <inputs> - <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/> - <param label="Restrict labels to standard rank assignments" name="mpa_format" truevalue="--mpa-format" falsevalue="" type="boolean" /> + <param name="input" type="data" format="tabular" label="Kraken output" + help="Select taxonomy classification produced by kraken"/> + <param name="mpa_format" type="boolean" truevalue="--mpa-format" falsevalue="" + label="Restrict labels to standard rank assignments" /> + <expand macro="input_database" /> </inputs> <outputs> - <data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" /> + <data name="translated" format="tabular" label="${tool.name} on ${on_string}: Translated classification"/> </outputs> <tests> <test> @@ -30,8 +33,7 @@ <output name="translated" file="kraken_translate_test1_output.tab" ftype="tabular"/> </test> </tests> - <help> - <![CDATA[ + <help><![CDATA[ .. class:: warningmark @@ -54,7 +56,6 @@ SEQ1 d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate. - ]]> - </help> + ]]></help> <expand macro="citations" /> </tool> |
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| diff -r b9971bca4b01 -r 9bdcba262627 macros.xml --- a/macros.xml Wed Mar 23 11:02:57 2016 -0400 +++ b/macros.xml Mon Aug 07 17:29:45 2017 -0400 |
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| @@ -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> |
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| diff -r b9971bca4b01 -r 9bdcba262627 tool_dependencies.xml --- a/tool_dependencies.xml Wed Mar 23 11:02:57 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |