| Previous changeset 5:b2392a9dfb01 (2016-03-23) Next changeset 7:658d47fd33e3 (2018-09-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/kraken/ commit e8fc7c9dad5f583ad6763ecb9bd8c924832abacd |
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modified:
kraken.xml macros.xml |
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removed:
tool_dependencies.xml |
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| diff -r b2392a9dfb01 -r 2fdac3e78553 kraken.xml --- a/kraken.xml Wed Mar 23 10:55:18 2016 -0400 +++ b/kraken.xml Mon Aug 07 17:29:06 2017 -0400 |
| [ |
| b'@@ -1,5 +1,5 @@\n <?xml version="1.0"?>\n-<tool id="kraken" name="Kraken" version="1.2.1">\n+<tool id="kraken" name="Kraken" version="@WRAPPER_VERSION@">\n <description>\n assign taxonomic labels to sequencing reads\n </description>\n@@ -7,56 +7,56 @@\n <import>macros.xml</import>\n </macros>\n <expand macro="requirements" />\n- <expand macro="stdio" />\n <expand macro="version_command" />\n- <command>\n+ <command detect_errors="exit_code">\n <![CDATA[\n @SET_DATABASE_PATH@ &&\n- kraken --threads \\${GALAXY_SLOTS:-1} @INPUT_DATABASE@ \n- \n- ${only_classified_output}\n+\n+ kraken\n+ --threads \\${GALAXY_SLOTS:-1}\n+ @INPUT_DATABASE@\n+ ${only_classified_output}\n \n- #if str( $quick_operation.quick ) == "yes":\n- --quick\n- --min-hits ${quick_operation.min_hits}\n+ #if str( $quick_operation.quick ) == "yes":\n+ --quick\n+ --min-hits ${quick_operation.min_hits}\n \n- #end if\n+ #end if\n \n- #if $single_paired.single_paired_selector == "yes":\n- #if $forward_input.is_of_type( \'fastq\' ):\n- --fastq-input\n- #else:\n- --fasta-input\n- #end if\n- "$forward_input" "$reverse_input"\n- ${single_paired.check_names}\n- #elif $single_paired.single_paired_selector == "collection":\n- #if $single_paired.input_pair.forward.is_of_type( \'fastq\' ):\n- --fastq-input\n+ #if $single_paired.single_paired_selector == \'yes\'\n+ #if $forward_input.is_of_type( \'fastq\' ):\n+ --fastq-input\n+ #else:\n+ --fasta-input\n+ #end if\n+ \'${single_paired.forward_input}\' \'${single_paired.reverse_input}\'\n+ ${single_paired.check_names}\n+ #elif $single_paired.single_paired_selector == "collection":\n+ #if $single_paired.input_pair.forward.is_of_type( \'fastq\' ):\n+ --fastq-input\n+ #else:\n+ --fasta-input\n+ #end if\n+ "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}"\n+ ${single_paired.check_names}\n #else:\n- --fasta-input\n- #end if\n- "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}"\n- ${single_paired.check_names}\n- #else:\n- #if $input_sequences.is_of_type( \'fastq\' ):\n- --fastq-input\n- #else:\n- --fasta-input\n+ #if $single_paired.input_sequences.is_of_type(\'fastq\')\n+ --fastq-input\n+ #else:\n+ --fasta-input\n+ #end if\n+ \'${single_paired.input_sequences}\'\n #end if\n- "$input_sequences"\n- #end if\n \n- #if $split_reads:\n- --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"\n- #end if\n+ #if $split_reads:\n+ --classified-out "${classified_out}" --unclassified-out "${unclassified_out}"\n+ #end if\n \n- ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output into STDOUT. This behavior can be re-created with test database provided in test-data/test_db/ folder. This is the reason for incrementing version number from 1.1.2 to 1.1.3\n+ ## The --output option was changed to redirect as it does not work properly is some situations. For example, on test database the tool classifies 4 reads but does not write them into a file if --output is specified. It does however print correct output in'..b'help="Quick mode: rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">\n <option value="yes">Yes</option>\n <option selected="True" value="no">No</option>\n </param>\n <when value="yes">\n- <param name="min_hits" type="integer" value="1" label="Number of hits required for classification" help="--min-hits; min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>\n+ <param name="min_hits" argument="--min-hits" type="integer" value="1" label="Number of hits required for classification"\n+ help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>\n </when>\n- <when value="no">\n- <!-- Do absolutely nothing -->\n- </when>\n+ <when value="no"/><!-- Do absolutely nothing -->\n </conditional>\n \n- <param name="only_classified_output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue="" label="Print no Kraken output for unclassified sequences" help="--only-classified-output"/>\n+ <param name="only_classified_output" argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue=""\n+ label="Print no Kraken output for unclassified sequences"/>\n \n <expand macro="input_database" />\n </inputs>\n <outputs>\n- <data format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads" name="classified_out">\n+ <data name="classified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads">\n <filter>(split_reads)</filter>\n </data>\n- <data format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads" name="unclassified_out">\n+ <data name="unclassified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">\n <filter>(split_reads)</filter>\n </data>\n- <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />\n+ <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>\n <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->\n </outputs>\n \n@@ -116,6 +117,7 @@\n <param name="quick" value="no"/>\n <param name="only-classified-output" value="false"/>\n <param name="kraken_database" value="test_db"/>\n+\n <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>\n </test>\n </tests>\n@@ -127,23 +129,6 @@\n \n -----\n \n-**Kraken options**\n-\n-The Galaxy version of Kraken implements the following options::\n-\n- \n- --fasta-input Input is FASTA format\n- --fastq-input Input is FASTQ format\n- --quick Quick operation (use first hit or hits)\n- --min-hits NUM In quick op., number of hits req\'d for classification\n- NOTE: this is ignored if --quick is not specified\n- --unclassified-out Print unclassified sequences to filename\n- --classified-out Print classified sequences to filename\n-\n- --only-classified-output Print no Kraken output for unclassified sequences\n- \n-------\n-\n **Output Format**\n \n Each sequence classified by Kraken results in a single line of output. Output lines contain five tab-delimited fields; from left to right, they are::\n' |
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| diff -r b2392a9dfb01 -r 2fdac3e78553 macros.xml --- a/macros.xml Wed Mar 23 10:55:18 2016 -0400 +++ b/macros.xml Mon Aug 07 17:29:06 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> |
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| diff -r b2392a9dfb01 -r 2fdac3e78553 tool_dependencies.xml --- a/tool_dependencies.xml Wed Mar 23 10:55:18 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> |