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author trinity_ctat
date Tue, 17 Jul 2018 11:50:42 -0400
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1 <tool id="ctat_trinity_rnaseq" name="ctat_trinity_rnaseq" version="1.0.0" profile="17.05">
2
3 <!-- Original tool written by Jeremy Goecks,
4 later development/maintenance by (in chronological order)
5 Brian Haas, Ben Fulton, Cicada Dennis
6 -->
7 <description>De novo assembly of RNA-Seq data using Trinity</description>
8 <requirements>
9 <requirement type="package" version="2.7">python</requirement>
10 <requirement type="package">subprocess32</requirement>
11 <requirement type="package">bzip2</requirement>
12 <requirement type="package" version="1.3.0">rsem</requirement>
13 <requirement type="package" version="3">bioconductor-edger</requirement>
14 <requirement type="package" version="2">bioconductor-qvalue</requirement>
15 <requirement type="package" version="2.6.6">trinity</requirement>
16 </requirements>
17 <command detect_errors="default">
18 <![CDATA[
19 python $__tool_directory__/ctat_trinity_wrapper.py
20 --CPU \${GALAXY_SLOTS:-4}
21 --max_memory \${TRINITY_MAX_MEMORY:-31G}
22 #if str($inputs.paired_or_single) == "paired":
23 --left $inputs.left_input --right $inputs.right_input
24 #if $inputs.left_input.ext == 'fasta':
25 --seqType fa
26 #else:
27 --seqType fq
28 #end if
29 #else:
30 --single $inputs.input
31 #if $inputs.input.ext == 'fasta':
32 --seqType fa
33 #else:
34 --seqType fq
35 #end if
36 #end if
37 ## direct to output
38 --timing trinity_out_dir/Trinity.timing
39 --log $trinity_log
40
41 ]]>
42 <!-- The fullpath, dir, and user options (preceed with dashes) can be
43 used in the ctat_trinity_wrapper.py command to create rerunable jobs.
44 We are not supporting rerunable jobs in this release of this tool.
45 fullpath \${TRINITY_RERUN_PREFIX}
46 dir '$adv.rerundir'
47 user $__user_id__
48 mem_per_cpu 31
49 -->
50 </command>
51 <stdio>
52 <exit_code range="1:" level="fatal" description="Program failed" />
53 <exit_code range=":-1" level="fatal" description="DRM killed job" />
54 </stdio>
55 <inputs>
56 <conditional name="inputs">
57 <param name="paired_or_single" type="select" label="Paired or Single-end data?">
58 <option value="paired">Paired</option>
59 <option value="single">Single</option>
60 </param>
61 <when value="paired">
62 <param format="fasta,fastq" name="left_input" type="data" label="Left/Forward strand reads" help=""/>
63 <param format="fasta,fastq" name="right_input" type="data" label="Right/Reverse strand reads" help=""/>
64 </when>
65 <when value="single">
66 <param format="fasta,fastq" name="input" type="data" label="Single-end reads" help=""/>
67 </when>
68 </conditional>
69 <!-- The following section was used to aid in creating rerunable jobs.
70 We are not supporting rerunable jobs in this release of this tool.
71 <section name="adv" title="Allow Job Rerun" expanded="False">
72 <param name="rerundir" type="txt" size="10" label="To make a job rerunnable, you will need to specify a unique tag to label the job, with no spaces or wierd characters." />
73 </section>
74 -->
75 </inputs>
76 <outputs>
77 <data format="txt" name="trinity_log" label="${tool.name} on ${on_string}: log" />
78 <data format="fasta" name="assembled_transcripts" label="${tool.name} on ${on_string}: Assembled Transcripts" from_work_dir="trinity_out_dir/Trinity.fasta"/>
79 </outputs>
80 <tests>
81 <!-- Not testing with the following inputs anymore.
82 <param name="left_input" value="FLI1.left.fq" />
83 <param name="right_input" value="FLI1.right.fq" />
84 -->
85 <test>
86 <param name="paired_or_single" value="paired" />
87 <param name="left_input" value="reads.left.simPE.fq" />
88 <param name="right_input" value="reads.right.simPE.fq" />
89 <!-- Not using in public version of tool
90 <param name="adv.rerundir" value="planemo_test_1" />
91 -->
92 <output name="trinity_log" >
93 <assert_contents>
94 <has_line_matching expression=".+" />
95 <has_line line="Trinity exited with status 0" />
96 </assert_contents>
97 </output>
98 <output name="assembled_transcripts" >
99 <assert_contents>
100 <has_line_matching expression=".+" />
101 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
102 </assert_contents>
103 </output>
104 </test>
105 <test>
106 <param name="paired_or_single" value="paired" />
107 <param name="left_input" value="Sp.cat_ds_hs.left.fq" />
108 <param name="right_input" value="Sp.cat_ds_hs.right.fq" />
109 <!-- Not using in public version of tool
110 <param name="adv.rerundir" value="planemo_test_2" />
111 -->
112 <!-- Following parameters are not used in this version of this tool. -->
113 <!--
114 <param name="JM" value="50G" />
115 <param name="CPU" value="2" />
116 <param name="library_type" value="None" />
117 <param name="group_pairs_distance" value="500" />
118 <param name="path_reinforcement_distance" value="75" />
119 <param name="use_additional" value="no" />
120 -->
121 <output name="trinity_log" >
122 <assert_contents>
123 <has_line_matching expression=".+" />
124 <has_line line="Trinity exited with status 0" />
125 </assert_contents>
126 </output>
127 <output name="assembled_transcripts" >
128 <assert_contents>
129 <has_line_matching expression=".+" />
130 <has_line_matching expression=">TRINITY.+?len=.+?path=.+" />
131 </assert_contents>
132 </output>
133 </test>
134 </tests>
135 <help>
136 This instance runs Trinity with the following command:
137
138 Trinity --max_memory 31G --CPU 4 --seqType seq_type --single singlefile or --left left_file --right right_file
139
140 Define TRINITY_MAX_MEMORY and GALAXY_SLOTS to change the default values for --max_memory and --CPU, respectively.
141
142 .. class:: infomark
143
144 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_.
145
146 .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
147 .. _here: https://github.com/trinityrnaseq/trinityrnaseq/wiki
148 </help>
149
150 <citations>
151 <citation type="doi">10.1038/nbt.1883</citation>
152 </citations>
153
154 </tool>