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comparison trinityrnaseq.xml @ 2:53b890343b67 draft

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author nate
date Mon, 26 Sep 2016 16:09:24 -0400
parents 976e99dd3c2b
children 3d072b99688e
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1:976e99dd3c2b 2:53b890343b67
12 <requirement type="package" version="2.2.0">trinity</requirement> 12 <requirement type="package" version="2.2.0">trinity</requirement>
13 </requirements> 13 </requirements>
14 <command> 14 <command>
15 MEM=`expr "\${GALAXY_SLOTS:-16}" \* 48 - 16` ; 15 MEM=`expr "\${GALAXY_SLOTS:-16}" \* 48 - 16` ;
16 16
17 workdir=`pwd`; 17 workdir=`pwd`;
18 echo "workdir is \$workdir"; 18 echo "workdir is \$workdir";
19 cd \$LOCAL; 19 cd \$LOCAL;
20 echo "Running Trinity from `pwd`"; 20 echo "Running Trinity from `pwd`";
21 21
22 Trinity --max_memory "\${MEM}G" 22 Trinity --max_memory "\${MEM}G"
23 --CPU "\${GALAXY_SLOTS:-16}" 23 --CPU "\${GALAXY_SLOTS:-16}"
24 --bflyHeapSpaceMax "32G" 24 --bflyHeapSpaceMax "32G"
25 --bflyHeapSpaceInit "2G" 25 --bflyHeapSpaceInit "2G"
26 --bflyGCThreads "6" 26 --bflyGCThreads "6"
27
28 #if $additional_params.use_additional == "yes" and $additional_params.normalize_reads == "yes":
29 --normalize_reads
30 #end if
27 31
28 ## Inputs. 32 ## Inputs.
29 #if str($inputs.paired_or_single) == "paired": 33 #if str($inputs.paired_or_single) == "paired":
30 --left $inputs.left_input --right $inputs.right_input 34 --left $inputs.left_input --right $inputs.right_input
31 #if $inputs.left_input.ext == 'fa': 35 #if $inputs.left_input.ext == 'fa':
109 <when value="yes"> 113 <when value="yes">
110 <param name="min_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" /> 114 <param name="min_kmer_cov" type="integer" value="1" min="1" label="inchworm_min_kmer_cov" help="Minimum kmer coverage required by Inchworm for initial contig construction" />
111 <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" /> 115 <param name="max_reads_per_graph" type="integer" value="20000000" min="10000" label="chrysalis_max_reads_per_graph" help="Maximum number of reads to be anchored within each transcript graph by Chrysalis" />
112 <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" /> 116 <param name="bfly_opts" type="text" value="None" label="bfly_opts" help="Options to pass on to Butterfly" />
113 <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/> 117 <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
118 <param name="min_contig_length" type="integer" value="200" min="1" label="Minimum Contig Length" help=""/>
119 <param name="normalize_reads" type="boolean" truevalue="yes" falsevalue="no" help="(--normalize_reads) Normalize reads, can decrease runtime and memory requirements for datasets exceeding 300M pairs"/>
114 </when> 120 </when>
115 </conditional> 121 </conditional>
116 </inputs> 122 </inputs>
117 <outputs> 123 <outputs>
118 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" /> 124 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />