Mercurial > repos > devteam > kraken
comparison kraken.xml @ 2:642f30185af2 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken/ commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:50:49 -0500 |
parents | 7b3ef9b4af80 |
children | 7c41dbaa9875 |
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1:7b3ef9b4af80 | 2:642f30185af2 |
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1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
2 <tool id="kraken" name="Kraken" version="1.1.1"> | 2 <tool id="kraken" name="Kraken" version="1.1.2"> |
3 <description> | 3 <description> |
4 assign taxonomic labels to sequencing reads | 4 assign taxonomic labels to sequencing reads |
5 </description> | 5 </description> |
6 <macros> | 6 <macros> |
7 <import>macros.xml</import> | 7 <import>macros.xml</import> |
25 #else: | 25 #else: |
26 --fasta-input | 26 --fasta-input |
27 #end if | 27 #end if |
28 "$forward_input" "$reverse_input" | 28 "$forward_input" "$reverse_input" |
29 ${single_paired.check_names} | 29 ${single_paired.check_names} |
30 #elif $single_paired.single_paired_selector == "collection": | |
31 #if $single_paired.input_pair.forward.is_of_type( 'fastq' ): | |
32 --fastq-input | |
33 #else: | |
34 --fasta-input | |
35 #end if | |
36 "${single_paired.input_pair.forward}" "${single_paired.input_pair.reverse}" | |
37 ${single_paired.check_names} | |
30 #else: | 38 #else: |
31 #if $input_sequences.is_of_type( 'fastq' ): | 39 #if $input_sequences.is_of_type( 'fastq' ): |
32 --fastq-input | 40 --fastq-input |
33 #else: | 41 #else: |
34 --fasta-input | 42 --fasta-input |
43 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}" | 51 ##kraken-translate --db ${kraken_database.fields.name} "${output}" > "${translated}" |
44 ]]> | 52 ]]> |
45 </command> | 53 </command> |
46 <inputs> | 54 <inputs> |
47 <conditional name="single_paired"> | 55 <conditional name="single_paired"> |
48 <param name="single_paired_selector" type="select" label="Reads are paired-end" help="--paired"> | 56 <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired"> |
57 <option value="collection">Collection</option> | |
49 <option value="yes">Yes</option> | 58 <option value="yes">Yes</option> |
50 <option selected="True" value="no">No</option> | 59 <option selected="True" value="no">No</option> |
51 </param> | 60 </param> |
61 <when value="collection"> | |
62 <param format="fasta,fastq" label="Collection of paired reads" name="input_pair" type="data_collection" collection_type="paired" help="FASTA or FASTQ datasets" /> | |
63 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" /> | |
64 </when> | |
52 <when value="yes"> | 65 <when value="yes"> |
53 <param format="fasta,fastq" label="Forward strand" name="forward_input" type="data" help="FASTA or FASTQ dataset"/> | 66 <param format="fasta,fastq" label="Forward strand" name="forward_input" type="data" help="FASTA or FASTQ dataset"/> |
54 <param format="fasta,fastq" label="Reverse strand" name="reverse_input" type="data" help="FASTA or FASTQ dataset"/> | 67 <param format="fasta,fastq" label="Reverse strand" name="reverse_input" type="data" help="FASTA or FASTQ dataset"/> |
55 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" /> | 68 <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" /> |
56 </when> | 69 </when> |