Mercurial > repos > devteam > hisat
changeset 2:4d91675e16e8 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat commit 00a7926c285bc4a339bd7deebf40b28f39c7d947
| author | devteam |
|---|---|
| date | Tue, 21 Jul 2015 15:33:45 -0400 |
| parents | 8bb3efa0dae8 |
| children | 0505bdb7d6b1 |
| files | hisat.xml |
| diffstat | 1 files changed, 5 insertions(+), 17 deletions(-) [+] |
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--- a/hisat.xml Tue Jul 21 15:33:12 2015 -0400 +++ b/hisat.xml Tue Jul 21 15:33:45 2015 -0400 @@ -1,4 +1,4 @@ -<tool id="hisat" name="HISAT" version="1.0.2"> +<tool id="hisat" name="HISAT" version="1.0.3"> <description>spliced aligner</description> <macros> <import>hisat_macros.xml</import> @@ -28,15 +28,6 @@ -1 "${reads_f}" -2 "${reads_r}" #else if str($input_format.paired.paired_selector) == 'paired_collection': -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}" - #else if str($input_format.paired.paired_selector) == 'paired_list': - #set forward_reads = [] - #set reverse_reads = [] - #for read in $input_format.paired.reads: - $forward_reads.append($read.forward) - $reverse_reads.append($read.reverse) - #end for - -1 "${','.join([str($read) for read in $forward_reads])}" - -2 "${','.join([str($read) for read in $reverse_reads])}" #else: -U "${reads}" #end if @@ -92,17 +83,14 @@ <conditional name="paired"> <expand macro="single_paired_selector" /> <when value="paired_collection"> - <param format="fastq,fastqsanger,fastqsolexa" name="reads" type="data_collection" collection_type="paired" label="Paired reads" /> - </when> - <when value="paired_list"> - <param format="fastq,fastqsanger,fastqsolexa" name="reads" type="data_collection" collection_type="list:paired" label="Paired reads" /> + <param format="fastq" name="reads" type="data_collection" collection_type="paired" label="Paired reads" /> </when> <when value="paired"> - <param label="Forward reads" type="data" name="reads_f" multiple="true" format="fastq,fastqsanger,fastqsolexa" /> - <param label="Reverse reads" type="data" name="reads_r" multiple="true" format="fastq,fastqsanger,fastqsolexa" /> + <param label="Forward reads" type="data" name="reads_f" multiple="true" format="fastq" /> + <param label="Reverse reads" type="data" name="reads_r" multiple="true" format="fastq" /> </when> <when value="single"> - <param label="Reads" type="data" name="reads" multiple="true" format="fastq,fastqsanger,fastqsolexa" /> + <param label="Reads" type="data" name="reads" multiple="true" format="fastq" /> </when> </conditional> </when>