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comparison trinity.xml @ 5:f976a93748a4 draft

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author trinity_ctat
date Tue, 29 Aug 2017 12:04:32 -0400
parents 3f5c7b49977d
children 4c1d32673942
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4:f4a429f40bfe 5:f976a93748a4
1 <tool id="trinityrnaseq" name="Trinity" version="2.4.0">
2
3 <!-- Originally written by Jeremy Goecks,
4 later maintained by (in chronological order)
5 bhaas, Ben Fulton, Cicada Dennis
6 -->
7 <description>De novo assembly of RNA-Seq data using Trinity 2.4.0</description>
8 <requirements>
9 <requirement type="package" version="2.4.0">trinity</requirement>
10 </requirements>
11 <command>
12 <![CDATA[
13 python $__tool_directory__/trinity_wrapper.py --mem_per_cpu 31
14 --CPU \${GALAXY_SLOTS:-4}
15 #if str($inputs.paired_or_single) == "paired":
16 --left $inputs.left_input --right $inputs.right_input
17 #if $inputs.left_input.ext == 'fasta':
18 --seqType fa
19 #else:
20 --seqType fq
21 #end if
22 #else:
23 --single $inputs.input
24 #if $inputs.input.ext == 'fasta':
25 --seqType fa
26 #else:
27 --seqType fq
28 #end if
29 #end if
30 ## direct to output
31 --timing trinity_out_dir/Trinity.timing
32 --user $__user_id__
33 --fullpath /N/dc2/scratch/tstrnity/rerun
34 --dir '$adv.rerundir'
35 --log $trinity_log
36
37 ]]>
38 </command>
39 <stdio>
40 <exit_code range="1:" level="fatal" description="Program failed" />
41 <exit_code range=":-1" level="fatal" description="DRM killed job" />
42 </stdio>
43 <inputs>
44 <conditional name="inputs">
45 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
46 <option value="paired">Paired</option>
47 <option value="single">Single</option>
48 </param>
49 <when value="paired">
50 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
51 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
52 </when>
53 <when value="single">
54 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
55 </when>
56 </conditional>
57 <section name="adv" title="Allow Job Rerun" expanded="False">
58 <param name="rerundir" type="text" size="10" label="To make a job rerunnable, you will need to specify a unique tag to label the job, with no spaces or wierd characters." />
59 </section>
60 </inputs>
61 <outputs>
62 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
63 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
64 </outputs>
65 <tests>
66 <!-- Not testing with the following inputs anymore.
67 <param name="left_input" value="FLI1.left.fq" />
68 <param name="right_input" value="FLI1.right.fq" />
69 -->
70 <test>
71 <param name="paired_or_single" value="paired" />
72 <param name="left_input" value="reads.left.simPE.fq" />
73 <param name="right_input" value="reads.right.simPE.fq" />
74 <param name="adv.rerundir" value="planemo_test_1" />
75 <output name="trinity_log" >
76 <assert_contents>
77 <has_line_matching expression=".+" />
78 <has_line line="Trinity exited with status 0" />
79 </assert_contents>
80 </output>
81 <output name="assembled_transcripts" >
82 <assert_contents>
83 <has_line_matching expression=".+" />
84 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
85 </assert_contents>
86 </output>
87 </test>
88 <test>
89 <param name="paired_or_single" value="paired" />
90 <param name="left_input" value="Sp.cat_ds_hs.left.fq" />
91 <param name="right_input" value="Sp.cat_ds_hs.right.fq" />
92 <param name="adv.rerundir" value="planemo_test_2" />
93 <!-- Following are not being used in this version of trinity.xml -->
94 <!--
95 <param name="paired_or_single" value="paired" />
96 <param name="left_input" file="cat_Sp.left.fq" />
97 <param name="right_input" file="cat_Sp.right.fq" />
98 <param name="JM" value="50G" />
99 <param name="CPU" value="2" />
100 <param name="library_type" value="None" />
101 <param name="group_pairs_distance" value="500" />
102 <param name="path_reinforcement_distance" va;ue="75" />
103 <param name="use_additional" value="no" />
104 -->
105 <output name="trinity_log" >
106 <assert_contents>
107 <has_line_matching expression=".+" />
108 <has_line line="Trinity exited with status 0" />
109 </assert_contents>
110 </output>
111 <output name="assembled_transcripts" >
112 <assert_contents>
113 <has_line_matching expression=".+" />
114 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
115 </assert_contents>
116 </output>
117 </test>
118 </tests>
119 <help>
120 This instance is running Trinity version 2.4.0 and uses the following command:
121
122 Trinity --max_memory 240G --CPU 8 --seqType seq_type --single singlefile or --left left_file --right right_file
123
124 .. class:: infomark
125
126 Trinity_, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. For more information, visit Trinity's wiki page here_.
127
128 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
129 .. _here: https://github.com/trinityrnaseq/trinityrnaseq/wiki
130 </help>
131
132 <citations>
133 <citation type="doi">10.1038/nbt.1883</citation>
134 </citations>
135
136 </tool>