Mercurial > repos > devteam > kraken
changeset 1:7b3ef9b4af80 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit 8fdf574819623961b1595461e906dd5a34e01add
| author | devteam |
|---|---|
| date | Wed, 04 Nov 2015 09:47:00 -0500 |
| parents | 0f17a8816b28 |
| children | 642f30185af2 |
| files | kraken.xml |
| diffstat | 1 files changed, 34 insertions(+), 11 deletions(-) [+] |
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--- a/kraken.xml Thu Jul 23 10:55:44 2015 -0400 +++ b/kraken.xml Wed Nov 04 09:47:00 2015 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="kraken" name="Kraken" version="1.1.0"> +<tool id="kraken" name="Kraken" version="1.1.1"> <description> assign taxonomic labels to sequencing reads </description> @@ -11,12 +11,6 @@ @SET_DATABASE_PATH@ && kraken --threads \${GALAXY_SLOTS:-1} @INPUT_DATABASE@ - #if $input_sequences.is_of_type( 'fastq' ): - --fastq-input - #else: - --fasta-input - #end if - ${only_classified_output} #if str( $quick_operation.quick ) == "yes": @@ -25,7 +19,22 @@ #end if - "$input_sequences" + #if $single_paired.single_paired_selector == "yes": + #if $forward_input.is_of_type( 'fastq' ): + --fastq-input + #else: + --fasta-input + #end if + "$forward_input" "$reverse_input" + ${single_paired.check_names} + #else: + #if $input_sequences.is_of_type( 'fastq' ): + --fastq-input + #else: + --fasta-input + #end if + "$input_sequences" + #end if #if $split_reads: --classified-out "${classified_out}" --unclassified-out "${unclassified_out}" @@ -35,7 +44,21 @@ ]]> </command> <inputs> - <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/> + <conditional name="single_paired"> + <param name="single_paired_selector" type="select" label="Reads are paired-end" help="--paired"> + <option value="yes">Yes</option> + <option selected="True" value="no">No</option> + </param> + <when value="yes"> + <param format="fasta,fastq" label="Forward strand" name="forward_input" type="data" help="FASTA or FASTQ dataset"/> + <param format="fasta,fastq" label="Reverse strand" name="reverse_input" type="data" help="FASTA or FASTQ dataset"/> + <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" /> + </when> + <when value="no"> + <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/> + </when> + + </conditional> <param label="Output classified and unclassified reads?" name="split_reads" type="boolean" help="Sets --unclassified-out and --classified-out"/> <conditional name="quick_operation"> @@ -56,10 +79,10 @@ <expand macro="input_database" /> </inputs> <outputs> - <data format="tabular" label="${tool.name} on ${on_string}: Classified reads" name="classified_out"> + <data format_source="input_sequences" label="${tool.name} on ${on_string}: Classified reads" name="classified_out"> <filter>(split_reads)</filter> </data> - <data format="tabular" label="${tool.name} on ${on_string}: Unclassified reads" name="unclassified_out"> + <data format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads" name="unclassified_out"> <filter>(split_reads)</filter> </data> <data format="tabular" label="${tool.name} on ${on_string}: Classification" name="output" />