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comparison trinity.xml @ 16:7c21b4380e84 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 7efdf3224552d113a01043ee5bf4517d770df933
author iuc
date Fri, 31 Mar 2017 11:32:51 -0400
parents ceacea4ee49e
children 87ab70ffdf1f
comparison
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15:1cf321b7ec23 16:7c21b4380e84
1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0"> 1 <tool id="trinity" name="Trinity" version="@WRAPPER_VERSION@.0">
2 <description>de novo assembly of RNA-Seq data</description> 2 <description>de novo assembly of RNA-Seq data</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 <requirement type="package" version="1.1.2">bowtie</requirement> 7 <command detect_errors="aggressive"><![CDATA[
8 <requirement type="set_environment">TRINITY_MEM_OPTIONS</requirement> 8 Trinity --no_version_check
9 </expand>
10 <expand macro="stdio"/>
11 <command><![CDATA[
12 Trinity
13 9
14 ## Inputs. 10 ## Inputs.
15 #if $inputs.paired_or_single == "paired": 11 #if $inputs.paired_or_single == "paired":
16 12
17 --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) } 13 --left ${ ','.join(['"%s"' % x for x in $inputs.left_input]) }
69 #if $additional_params.min_kmer_cov: 65 #if $additional_params.min_kmer_cov:
70 --min_kmer_cov $additional_params.min_kmer_cov 66 --min_kmer_cov $additional_params.min_kmer_cov
71 #end if 67 #end if
72 68
73 ## CPU and butterfly options. 69 ## CPU and butterfly options.
74 --CPU \${GALAXY_SLOTS:-4} \${TRINITY_MEM_OPTIONS:---max_memory 1G} --bfly_opts "-V 10 --stderr" 70 --CPU \${GALAXY_SLOTS:-4} --max_memory \${TRINITY_MAX_MEMORY:-1G} --bflyHeapSpaceMax \${TRINITY_MAX_MEMORY:-1G} --bfly_opts '-V 10 --stderr'
75 71
76 ## > $trinity_log 2>&1 72 ## > $trinity_log 2>&1
77
78 ]]></command> 73 ]]></command>
79 <inputs> 74 <inputs>
80 <conditional name="inputs"> 75 <conditional name="inputs">
81 <param name="paired_or_single" type="select" label="Paired or Single-end data?"> 76 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
82 <option value="paired">Paired</option> 77 <option value="paired">Paired</option>