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comparison kraken2.xml @ 8:d120504e741a draft

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planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/kraken2 commit 593a4002db3f2513974809a94db514c05fa589f6-dirty
author dfornika
date Mon, 04 Mar 2019 17:17:43 -0500
parents 7b9218c5e126
children a811afe91eab
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7:7b9218c5e126 8:d120504e741a
7 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">kraken2</requirement>
8 </requirements> 8 </requirements>
9 <version_command>kraken2 --version</version_command> 9 <version_command>kraken2 --version</version_command>
10 <command detect_errors="exit_code"> 10 <command detect_errors="exit_code">
11 <![CDATA[ 11 <![CDATA[
12 @SET_DATABASE_PATH@
12 kraken2 13 kraken2
13 --threads \${GALAXY_SLOTS:-1} 14 --threads \${GALAXY_SLOTS:-1}
14 --db '$kraken2_database' 15 --db '$kraken2_database'
15 #if $single_paired.single_paired_selector == 'yes' 16 #if $single_paired.single_paired_selector == 'yes'
16 '${single_paired.forward_input}' '${single_paired.reverse_input}' 17 '${single_paired.forward_input}' '${single_paired.reverse_input}'
33 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" /> 34 <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
34 </when> 35 </when>
35 <when value="yes"> 36 <when value="yes">
36 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/> 37 <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
37 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/> 38 <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
38 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />
39 </when> 39 </when>
40 <when value="no"> 40 <when value="no">
41 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/> 41 <param format="fasta,fastq" label="Input sequences" name="input_sequences" type="data" help="FASTA or FASTQ datasets"/>
42 </when> 42 </when>
43 </conditional> 43 </conditional>