Mercurial > repos > iuc > stacks_assembleperead
comparison stacks_assembleperead.xml @ 11:0c741f364d18 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 2b0a6546733e3e090b19e83f4a8b87e09bb11424"
author | iuc |
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date | Sun, 19 Jan 2020 06:37:54 -0500 |
parents | e6919d8ae34d |
children | 6eaf0f9836c8 |
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10:bc108981ca68 | 11:0c741f364d18 |
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1 <tool id="stacks_assembleperead" name="Stacks: assemble read pairs by locus" version="@WRAPPER_VERSION@.0"> | 1 <tool id="stacks_assembleperead" name="Stacks: assemble read pairs by locus" version="@WRAPPER_VERSION@.1"> |
2 <description>run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers</description> | 2 <description>run the STACKS sort_read_pairs.pl and exec_velvet.pl wrappers</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 | 9 |
10 mkdir stacks_inputs reads stacks_outputs | 10 mkdir stacks_inputs reads stacks_outputs |
11 | |
12 && | 11 && |
13 | |
14 #for $input_file in $stacks_col | 12 #for $input_file in $stacks_col |
15 #set $ext = "" | 13 #set $ext = "" |
16 #if not str($input_file.element_identifier).endswith('.tsv') | 14 #if not str($input_file.element_identifier).endswith('.tsv') |
17 #set $ext = ".tsv" | 15 #set $ext = ".tsv" |
18 #end if | 16 #end if |
49 | 47 |
50 -o stacks_outputs | 48 -o stacks_outputs |
51 | 49 |
52 #if $velvet.use_velvet == "yes" | 50 #if $velvet.use_velvet == "yes" |
53 ## remove possible empty files | 51 ## remove possible empty files |
54 && find stacks_outputs -type f -size 0 -delete | 52 && find stacks_outputs -type f -size 0 -exec rm {} \; |
55 | 53 |
56 && | 54 && |
57 mkdir assembled | 55 mkdir assembled |
58 && | 56 && |
59 velvet_path=`which velveth` && velvet_path=`dirname "\$velvet_path"` | 57 velvet_path=`which velveth` && velvet_path=`dirname "\$velvet_path"` |