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Upload ctat tools.
author trinity_ctat
date Tue, 17 Jul 2018 11:49:16 -0400
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-1:000000000000 0:a940c4a36a43
1 <tool id="ctat_lncrna" name="ctat_lncrna" version="1.0.0" profile="17.05">
2
3 <description>Filters a high-quality set of lncRNA from reconstructed RNA-seq data</description>
4 <requirements>
5 <requirement type="package" version="1.0.1">ctat-lncrna</requirement>
6 </requirements>
7 <command detect_errors="default">
8 <![CDATA[
9 #if str($bedfile) != "":
10 lncrna --bedfile $bedfile
11 --config "${assembly.fields.path}"
12 #end if
13
14 #if str($assembly) != "":
15 --assembly "${assembly.fields.value}"
16 #end if
17
18 #if $min_overlap != "":
19 --min_overlap "$min_overlap"
20 #end if
21
22 #if str($min_cluster) != "":
23 --min_cluster "$min_cluster"
24 #end if
25
26 #if str($min_coding) != "":
27 --min_coding "$min_coding"
28 #end if
29
30 #if str($minMatch) != "":
31 --minMatch "$minMatch"
32 #end if
33
34 #if str($pad) != "":
35 --pad "$pad"
36 #end if
37
38 #if str($gap_open) != "":
39 --gap_open "$gap_open"
40 #end if
41
42 #if str($gap_extend) != "":
43 --gap_extend "$gap_extend"
44 #end if
45 --web
46 && cp -r slncky.EvolutionBrowser $html_file.files_path
47 ]]>
48 </command>
49
50 <inputs>
51 <param name="bedfile" format="interval" type="data" value="bedfile" label="Bed File:" help="Reconstructed transcripts (ex. from StringTie or Trinity)"/>
52 <param name="min_overlap" type="float" value="0.0" label="Min overlap" help="Remove any transcript that overlap annotated coding gene greater than min_overlap" />
53 <param name="min_cluster" type="integer" value="2" label="Min cluster" help="Minimum size of duplication clusters to remove" />
54 <param name="min_coding" type="float" value="0.1" label="Min exonic identity to filter out transcript that aligns to orthologous coding gene" help="default is set by learning coding alignment distribution from data"/>
55 <param name="minMatch" type="float" value="0.1" label="Min match" help="Minimum match parameter for liftover" />
56 <param name="pad" type="integer" value="0" label="Pad" help="No. of basepairs to search up- and down-stream when lifting over lnc to ortholog" />
57 <param name="gap_open" type="integer" value="200" label="Gap open penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search"/>
58 <param name="gap_extend" type="integer" value="40" label="Gap extend penalty to pass to lastz" help="Decreasing this parameter will increase sensitivity of orthology search."/>
59 <param name="assembly" type="select" label="Choose annotation:" help="Select annotation">
60 <options from_data_table="ctat_lncrna_annotations" />
61 </param>
62 </inputs>
63
64 <outputs>
65 <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/>
66 <data format="tabular" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/>
67 <data format="tabular" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/>
68 <data format="tabular" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/>
69 <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/>
70 <data format="tabular" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/>
71 <data format="tabular" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/>
72 <data format="tabular" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/>
73 <data format="tabular" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/>
74 </outputs>
75
76 <stdio>
77 <exit_code range="1:" level="fatal" description="Error in SLNCky" />
78 </stdio>
79
80 <tests>
81 <test>
82 <param name="bedfile" value="reads.simPE.StringTie.transcripts.bed" />
83 <param name="assembly" value="hg19" />
84 <param name="min_overlap" value="0.0" />
85 <param name="min_cluster" value="2" />
86 <param name="min_coding" value="0.1" />
87 <param name="minMatch" value="0.1" />
88 <param name="pad" value="0" />
89 <param name="gap_open" value="200" />
90 <param name="gap_extend" value="40" />
91
92 <!-- <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/> -->
93 <output name="html_file" file="slncky/reads.simPE.browse.html" />
94
95 <!-- <data format="txt" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> -->
96 <output name="canonical_to_lncs" file="slncky/reads.simPE.canonical_to_lncs.txt" />
97
98 <!-- <data format="txt" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> -->
99 <output name="cluster_info" file="slncky/reads.simPE.cluster_info.txt" />
100
101 <!-- <data format="txt" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> -->
102 <output name="filtered_info" file="slncky/reads.simPE.filtered_info.txt" />
103
104 <!-- <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/> -->
105 <output name="lncs" file="slncky/reads.simPE.lncs.bed" />
106
107 <!-- <data format="txt" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> -->
108 <output name="lncs_info" file="slncky/reads.simPE.lncs.info.txt" />
109
110 <!-- <data format="txt" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> -->
111 <output name="orfs" file="slncky/reads.simPE.orfs.txt" />
112
113 <!-- <data format="txt" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> -->
114 <output name="orthologs_top" file="slncky/reads.simPE.orthologs.top.txt" />
115
116 <!-- <data format="txt" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> -->
117 <output name="orthologs" file="slncky/reads.simPE.orthologs.txt" />
118
119 </test>
120 <test>
121 <param name="bedfile" value="mir-17-92.StringTie.transcripts.bed" />
122 <param name="assembly" value="hg19" />
123 <param name="min_overlap" value="0.0" />
124 <param name="min_cluster" value="2" />
125 <param name="min_coding" value="0.1" />
126 <param name="minMatch" value="0.1" />
127 <param name="pad" value="0" />
128 <param name="gap_open" value="200" />
129 <param name="gap_extend" value="40" />
130
131 <!-- <data format="html" name="html_file" label="web_report" from_work_dir="slncky.EvolutionBrowser/browse.html"/> -->
132 <output name="html_file" file="slncky/mir-17-92.browse.html" />
133
134 <!-- <data format="txt" name="canonical_to_lncs" label="canonical_to_lncs" from_work_dir="slncky.canonical_to_lncs.txt"/> -->
135 <output name="canonical_to_lncs" file="slncky/mir-17-92.canonical_to_lncs.txt.sorted" sort="true" />
136
137 <!-- <data format="txt" name="cluster_info" label="cluster_info" from_work_dir="slncky.cluster_info.txt"/> -->
138 <!-- This file isn't being created for some reason...
139 <output name="cluster_info" >
140 <assert_contents>
141 <has_line_matching expression=".+" />
142 </assert_contents>
143 </output>
144 -->
145
146 <!-- <data format="txt" name="filtered_info" label="filtered_info" from_work_dir="slncky.filtered_info.txt"/> -->
147 <output name="filtered_info" file="slncky/mir-17-92.filtered_info.txt.sorted" sort="true" />
148
149 <!-- <data format="bed" name="lncs" label="lncs" from_work_dir="slncky.lncs.bed"/> -->
150 <output name="lncs" file="slncky/mir-17-92.lncs.bed" />
151
152 <!-- <data format="txt" name="lncs_info" label="lncs.info" from_work_dir="slncky.lncs.info.txt"/> -->
153 <output name="lncs_info" file="slncky/mir-17-92.lncs.info.txt" />
154
155 <!-- <data format="txt" name="orfs" label="orfs" from_work_dir="slncky.orfs.txt"/> -->
156 <output name="orfs" file="slncky/mir-17-92.orfs.txt" />
157
158 <!-- <data format="txt" name="orthologs_top" label="orthologs.top" from_work_dir="slncky.orthologs.top.txt"/> -->
159 <output name="orthologs_top" file="slncky/mir-17-92.orthologs.top.txt" />
160
161 <!-- <data format="txt" name="orthologs" label="orthologs" from_work_dir="slncky.orthologs.txt"/> -->
162 <output name="orthologs" file="slncky/mir-17-92.orthologs.txt" />
163 </test>
164 </tests>
165
166 <help>
167 .. class:: infomark
168
169 slncky is a tool for lncRNA discovery from RNA-Seq data. slncky filters a high-quality set of noncoding transcripts, discovers lncRNA orthologs, and characterizes conserved lncRNA evolution.
170
171 To learn more about slncky visit their website_ .
172
173 .. _website: https://github.com/slncky/slncky
174
175 </help>
176
177 <citations>
178 <citation type="doi">10.1186/s13059-016-0880-9</citation>
179 </citations>
180
181 </tool>