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comparison trinity.xml @ 20:875e118b5f1c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550
author iuc
date Mon, 22 Jan 2018 11:22:08 -0500
parents f07bc380d66c
children 3867ecd957f7
comparison
equal deleted inserted replaced
19:f07bc380d66c 20:875e118b5f1c
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 <command detect_errors="aggressive"><![CDATA[ 7 <command detect_errors="aggressive"><![CDATA[
8 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
9 GALAXY_MEMORY_GB=1 ;
10 else
11 GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ;
12 fi ;
13
14 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
15 workdir=`pwd` ;
16 cd "\$TRINITY_SCRATCH_DIR" ;
17 fi ;
18
8 #if $additional_params.guided.is_guided == "yes": 19 #if $additional_params.guided.is_guided == "yes":
9 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' && 20 ln -s '${$additional_params.guided.genome_guided_bam}' 'localbam.bam' &&
10 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' && 21 ln -s '${$additional_params.guided.genome_guided_bam.metadata.bam_index}' 'localbam.bam.bai' &&
11 #end if 22 #end if
12 Trinity --no_version_check 23 Trinity --no_version_check
82 #if $additional_params.min_kmer_cov: 93 #if $additional_params.min_kmer_cov:
83 --min_kmer_cov $additional_params.min_kmer_cov 94 --min_kmer_cov $additional_params.min_kmer_cov
84 #end if 95 #end if
85 96
86 ## CPU and butterfly options. 97 ## CPU and butterfly options.
87 --CPU \${GALAXY_SLOTS:-4} --max_memory \${TRINITY_MAX_MEMORY:-1G} --bflyHeapSpaceMax \${TRINITY_MAX_MEMORY:-1G} --bfly_opts '-V 10 --stderr' 98 --CPU \${GALAXY_SLOTS:-4} --max_memory \${GALAXY_MEMORY_GB:-1}G --bflyHeapSpaceMax \${GALAXY_MEMORY_GB:-1}G --bfly_opts '-V 10 --stderr'
88 99
89 ## > $trinity_log 2>&1 100 ## > $trinity_log 2>&1
101
102 &&
103
104 if [ ! -z "\$TRINITY_SCRATCH_DIR" ] ; then
105 mkdir -p "\$workdir/trinity_out_dir";
106 cp -p trinity_out_dir/Trinity* "\$workdir/trinity_out_dir";
107 cd "\$workdir";
108 fi ;
109
90 ]]></command> 110 ]]></command>
91 <inputs> 111 <inputs>
92 <conditional name="inputs"> 112 <conditional name="inputs">
93 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 113 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
94 <option value="single">Single-end</option> 114 <option value="single">Single-end</option>