Mercurial > repos > iuc > data_manager_hisat2_index_builder

comparison data_manager/hisat2_index_builder.xml @ 1:b13b84cb11b5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_hisat2_index_builder commit feb20045fb10de6cce2517784f52672322d4d9f8-dirty
author iuc
date Sat, 10 Oct 2015 16:01:18 -0400
parents d3eb4d51b285
children 4014cb2c17db
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0:d3eb4d51b285 1:b13b84cb11b5
6 <stdio> 6 <stdio>
7 <exit_code range=":-1" /> 7 <exit_code range=":-1" />
8 <exit_code range="1:" /> 8 <exit_code range="1:" />
9 </stdio> 9 </stdio>
10 <command><![CDATA[ 10 <command><![CDATA[
11 #if $gtf_input: 11 #if $advanced.adv_param_select == 'yes' and $gtf_input:
12 ln -s "${gtf_input}" gtf_file.gtf && 12 ln -s "${gtf_input}" gtf_file.gtf &&
13 python \$HISAT2_ROOT_DIR/bin/extract_splice_sites.py gtf_file.gtf > splice_sites.txt && 13 python \$HISAT2_ROOT_DIR/bin/extract_splice_sites.py gtf_file.gtf > splice_sites.txt &&
14 python \$HISAT2_ROOT_DIR/bin/extract_exons.py gtf_file.gtf > exon.txt && 14 python \$HISAT2_ROOT_DIR/bin/extract_exons.py gtf_file.gtf > exon.txt &&
15 ls -lh && 15 ls -lh &&
16 #end if 16 #end if
17 #if $snps: 17 #if $advanced.adv_param_select == 'yes' and $snps:
18 ln -s "${all_fasta_source.fields.path}" genome.fa && 18 ln -s "${all_fasta_source.fields.path}" genome.fa &&
19 ln -s "${snps}" snps.tabular && 19 ln -s "${snps}" snps.tabular &&
20 python \$HISAT2_ROOT_DIR/bin/extract_snps.py --genome_file genome.fa --snp_file snps.tabular > snps.txt && 20 python \$HISAT2_ROOT_DIR/bin/extract_snps.py --genome_file genome.fa --snp_file snps.tabular > snps.txt &&
21 #end if 21 #end if
22 python $__tool_directory__/hisat2_index_builder.py --output "${out_file}" 22 python $__tool_directory__/hisat2_index_builder.py --output "${out_file}"