Mercurial > repos > dfornika > kraken2
diff kraken2.xml @ 7:7b9218c5e126 draft
planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit 593a4002db3f2513974809a94db514c05fa589f6-dirty
| author | dfornika |
|---|---|
| date | Mon, 04 Mar 2019 17:07:17 -0500 |
| parents | 6a9137c96822 |
| children | d120504e741a |
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--- a/kraken2.xml Mon Mar 04 16:57:25 2019 -0500 +++ b/kraken2.xml Mon Mar 04 17:07:17 2019 -0500 @@ -11,31 +11,14 @@ <![CDATA[ kraken2 --threads \${GALAXY_SLOTS:-1} + --db '$kraken2_database' #if $single_paired.single_paired_selector == 'yes' - #if $forward_input.is_of_type( 'fastq' ): - --fastq-input - #else: - --fasta-input - #end if '${single_paired.forward_input}' '${single_paired.reverse_input}' - ${single_paired.check_names} #elif $single_paired.single_paired_selector == "collection": - #if $single_paired.input_pair.forward.is_of_type( 'fastq' ): - --fastq-input - #else: - --fasta-input - #end if '${single_paired.input_pair.forward}' '${single_paired.input_pair.reverse}' - ${single_paired.check_names} #else: - #if $single_paired.input_sequences.is_of_type('fastq') - --fastq-input - #else: - --fasta-input - #end if '${single_paired.input_sequences}' #end if - --db '$kraken2_database' > '$output' ]]> </command> @@ -48,7 +31,6 @@ </param> <when value="collection"> <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" /> - <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/> </when> <when value="yes"> <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>