|
0
|
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>
|
