Mercurial > repos > devteam > hisat

comparison hisat.xml @ 2:4d91675e16e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
1:8bb3efa0dae8 2:4d91675e16e8
1 <tool id="hisat" name="HISAT" version="1.0.2"> 1 <tool id="hisat" name="HISAT" version="1.0.3">
2 <description>spliced aligner</description> 2 <description>spliced aligner</description>
3 <macros> 3 <macros>
4 <import>hisat_macros.xml</import> 4 <import>hisat_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
26 hisat -p \${GALAXY_SLOTS:-1} -x "${index_path}" 26 hisat -p \${GALAXY_SLOTS:-1} -x "${index_path}"
27 #if str($input_format.paired.paired_selector) == 'paired': 27 #if str($input_format.paired.paired_selector) == 'paired':
28 -1 "${reads_f}" -2 "${reads_r}" 28 -1 "${reads_f}" -2 "${reads_r}"
29 #else if str($input_format.paired.paired_selector) == 'paired_collection': 29 #else if str($input_format.paired.paired_selector) == 'paired_collection':
30 -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}" 30 -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"
31 #else if str($input_format.paired.paired_selector) == 'paired_list':
32 #set forward_reads = []
33 #set reverse_reads = []
34 #for read in $input_format.paired.reads:
35 $forward_reads.append($read.forward)
36 $reverse_reads.append($read.reverse)
37 #end for
38 -1 "${','.join([str($read) for read in $forward_reads])}"
39 -2 "${','.join([str($read) for read in $reverse_reads])}"
40 #else: 31 #else:
41 -U "${reads}" 32 -U "${reads}"
42 #end if 33 #end if
43 #if $input_format.input_format_selector == 'fasta': 34 #if $input_format.input_format_selector == 'fasta':
44 -f 35 -f
90 </when> 81 </when>
91 <when value="fastq"> 82 <when value="fastq">
92 <conditional name="paired"> 83 <conditional name="paired">
93 <expand macro="single_paired_selector" /> 84 <expand macro="single_paired_selector" />
94 <when value="paired_collection"> 85 <when value="paired_collection">
95 <param format="fastq,fastqsanger,fastqsolexa" name="reads" type="data_collection" collection_type="paired" label="Paired reads" /> 86 <param format="fastq" name="reads" type="data_collection" collection_type="paired" label="Paired reads" />
96 </when>
97 <when value="paired_list">
98 <param format="fastq,fastqsanger,fastqsolexa" name="reads" type="data_collection" collection_type="list:paired" label="Paired reads" />
99 </when> 87 </when>
100 <when value="paired"> 88 <when value="paired">
101 <param label="Forward reads" type="data" name="reads_f" multiple="true" format="fastq,fastqsanger,fastqsolexa" /> 89 <param label="Forward reads" type="data" name="reads_f" multiple="true" format="fastq" />
102 <param label="Reverse reads" type="data" name="reads_r" multiple="true" format="fastq,fastqsanger,fastqsolexa" /> 90 <param label="Reverse reads" type="data" name="reads_r" multiple="true" format="fastq" />
103 </when> 91 </when>
104 <when value="single"> 92 <when value="single">
105 <param label="Reads" type="data" name="reads" multiple="true" format="fastq,fastqsanger,fastqsolexa" /> 93 <param label="Reads" type="data" name="reads" multiple="true" format="fastq" />
106 </when> 94 </when>
107 </conditional> 95 </conditional>
108 </when> 96 </when>
109 </conditional> 97 </conditional>
110 <conditional name="reference_genome"> 98 <conditional name="reference_genome">