Mercurial > repos > iuc > stacks_genotypes
comparison stacks_genotypes.xml @ 3:aa333a0a7d5a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author | iuc |
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date | Sat, 25 Jun 2016 17:28:58 -0400 |
parents | 26e7ae6adec0 |
children | 969a09779e3c |
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2:dbe3901aace2 | 3:aa333a0a7d5a |
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1 <tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.0"> | 1 <tool id="stacks_genotypes" name="Stacks: genotypes" version="@WRAPPER_VERSION@.1"> |
2 <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description> | 2 <description>analyse haplotypes or genotypes in a genetic cross ('genotypes' program)</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements"/> | 6 <expand macro="requirements"/> |
7 <expand macro="stdio"/> | 7 <expand macro="stdio"/> |
8 <command><![CDATA[ | 8 <command><![CDATA[ |
9 #import re | |
9 | 10 |
10 mkdir stacks_outputs | 11 mkdir stacks_outputs |
11 | 12 |
12 && | 13 && |
13 | 14 |
14 #for $input_file in $input_col: | 15 #for $input_file in $input_col: |
15 #set $ext = "" | 16 #set $filename = str($input_file.element_identifier) |
16 #if not str($input_file.name).endswith('.tsv'): | 17 #if not $filename.endswith('.tsv'): |
17 #set $ext = ".tsv" | 18 #set $filename = $filename + ".tsv" |
18 #end if | 19 #end if |
19 ln -s "${input_file}" "stacks_outputs/${input_file.name}${ext}" && | 20 #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename): |
21 ln -s "${input_file}" "stacks_outputs/${filename}" && | |
22 #end if | |
20 #end for | 23 #end for |
21 | 24 |
22 genotypes | 25 genotypes |
23 | 26 |
24 -P stacks_outputs | 27 -P stacks_outputs |