Mercurial > repos > iuc > stacks_assembleperead

comparison stacks_assembleperead.xml @ 11:0c741f364d18 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 2b0a6546733e3e090b19e83f4a8b87e09bb11424"
author iuc
date Sun, 19 Jan 2020 06:37:54 -0500
parents e6919d8ae34d
children 6eaf0f9836c8
comparison
equal deleted inserted replaced
10:bc108981ca68 11:0c741f364d18
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"`