Mercurial > repos > rnateam > mirdeep2
comparison mirdeep2.xml @ 0:eaac585f172a draft
Imported from capsule None
author | rnateam |
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date | Tue, 27 Jan 2015 09:06:24 -0500 |
parents | |
children | b21be04f52e4 |
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1 <tool id="rbc_mirdeep2" name="MiRDeep2" version="2.0.0"> | |
2 <description> | |
3 <![CDATA[ | |
4 identification of novel and known miRNAs | |
5 ]]> | |
6 </description> | |
7 <requirements> | |
8 <requirement type="package" version="2.0">mirdeep2</requirement> | |
9 <requirement type="package" version="2.0">mirdeep2_quantifier</requirement> | |
10 <requirement type="package" version="0.12.7">bowtie</requirement> | |
11 <requirement type="package" version="5.18.1">perl</requirement> | |
12 <requirement type="package" version="1.8.5">vienna_rna</requirement> | |
13 <requirement type="package" version="2.023">pdf_api2</requirement> | |
14 <requirement type="package" version="2.0">randfold</requirement> | |
15 </requirements> | |
16 | |
17 <command> | |
18 <![CDATA[ | |
19 miRDeep2.pl | |
20 | |
21 $reads | |
22 $genome | |
23 $mappings | |
24 | |
25 #if $mature_this | |
26 $mature_this | |
27 #else | |
28 none | |
29 #end if | |
30 | |
31 #if $mature_other | |
32 $mature_other | |
33 #else | |
34 none | |
35 #end if | |
36 | |
37 #if $precursors | |
38 $precursors | |
39 #else | |
40 none | |
41 #end if | |
42 | |
43 #if $species.value != 'all' | |
44 -t $species | |
45 #end if | |
46 | |
47 #if $star_sequences | |
48 -s $star_sequences | |
49 #end if | |
50 | |
51 #if $min_read_stack | |
52 -a $min_read_stack | |
53 #end if | |
54 | |
55 #if $min_read_stack | |
56 -a $min_read_stack | |
57 #end if | |
58 | |
59 -g $max_precursors_analyze | |
60 -b $min_score_cutoff | |
61 $disable_randfold | |
62 | |
63 ; cp result*.bed result.bed 2> /dev/null | |
64 ; cp result*.csv result.csv 2> /dev/null | |
65 ; cp mirdeep_runs/run*/output.mrd . 2> /dev/null | |
66 ; cp mirdeep_runs/run*/survey.csv . 2> /dev/null | |
67 | |
68 ## html output | |
69 ; | |
70 cp result*.html $html 2> /dev/null | |
71 | |
72 ## move pdf directory to be accessible from the new index.html | |
73 ; | |
74 mkdir -p $html.files_path 2> /dev/null | |
75 ; | |
76 cp -R pdfs* $html.files_path 2> /dev/null | |
77 | |
78 ]]> | |
79 </command> | |
80 <stdio> | |
81 <!-- Anything other than zero is an error --> | |
82 <exit_code range="1:" /> | |
83 <exit_code range=":-1" /> | |
84 <!-- In case the return code has not been set propery check stderr too --> | |
85 <regex match="Error:" /> | |
86 <regex match="Exception:" /> | |
87 </stdio> | |
88 <inputs> | |
89 <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads"> | |
90 <help> | |
91 <![CDATA[ | |
92 Reads in fasta format. The identifier should contain a prefix, a running | |
93 number and a '_x' to indicate the number of reads that have this sequence. | |
94 There should be no redundancy in the sequences. | |
95 ]]> | |
96 </help> | |
97 </param> | |
98 <param name="genome" format="fasta" type="data" label="Genome" help="Genome contigs in fasta format. The identifiers should be unique."/> | |
99 <param name="mappings" format="tabular" type="data" label="Mappings" help="Reads mapped against genome. Mappings should be in ARF format."/> | |
100 <param name="mature_this" optional="true" format="fasta" type="data" label="Mature miRNA sequences for this species" | |
101 help="miRBase miRNA sequences in fasta format. These should be the known mature sequences for the species being analyzed."/> | |
102 <param name="mature_other" optional="true" format="fasta" type="data" label="Mature miRNA sequences for related species"> | |
103 <help> | |
104 <![CDATA[ | |
105 miRBase miRNA sequences in fasta format. These should be the pooled known | |
106 mature sequences for 1-5 species closely related to the species being analyzed. | |
107 ]]> | |
108 </help> | |
109 </param> | |
110 <param name="precursors" optional="true" format="fasta" type="data" label="Precursor sequences" | |
111 help="miRBase miRNA precursor sequences in fasta format. These should be the known precursor sequences for the species being analyzed."/> | |
112 | |
113 <param name="species" type="select" label="Search in species" help="If not searching in a specific species all species in your files will be analyzed. (-t)"> | |
114 <option value="all">All species</option> | |
115 <option value="tni">tetraodon</option> | |
116 <option value="dps">d.pseudoobscura</option> | |
117 <option value="dya">d.yakuba</option> | |
118 <option value="ame">a.mellifera</option> | |
119 <option value="dmo">d.mojavensis</option> | |
120 <option value="cel">worm</option> | |
121 <option value="aga">a.gambiae</option> | |
122 <option value="cbr">c.briggsae</option> | |
123 <option value="cin">c.intestinalis</option> | |
124 <option value="mmu">mouse</option> | |
125 <option value="xtr">x.tropicalis</option> | |
126 <option value="eca">horse</option> | |
127 <option value="cfa">dog</option> | |
128 <option value="fru">fugu</option> | |
129 <option value="bta">cow</option> | |
130 <option value="der">d.erecta</option> | |
131 <option value="dgr">d.grimshawi</option> | |
132 <option value="gga">chicken</option> | |
133 <option value="spu">s.purpuratus</option> | |
134 <option value="bfl">lancelet</option> | |
135 <option value="ptr">chimp</option> | |
136 <option value="dse">d.sechellia</option> | |
137 <option value="dpe">d.persimilis</option> | |
138 <option value="dvi">d.virilis</option> | |
139 <option value="rno">rat</option> | |
140 <option value="dme">d.melanogaster</option> | |
141 <option value="lca">cat</option> | |
142 <option value="sja">c.japonica</option> | |
143 <option value="dan">d.ananassae</option> | |
144 <option value="hsa">human</option> | |
145 <option value="dsi">d.simulans</option> | |
146 </param> | |
147 <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/> | |
148 | |
149 <param name="min_read_stack" optional="true" type="integer" minvalue="0" label="Minimum read stack height"> | |
150 <help> | |
151 <![CDATA[ | |
152 minimum read stack height that triggers analysis. Using this option disables | |
153 automatic estimation of the optimal value and all detected precursors are analyzed. (-a) | |
154 ]]> | |
155 </help> | |
156 </param> | |
157 <param name="max_precursors_analyze" type="integer" value="50000" label="Maximum precursors" | |
158 help="Maximum number of precursors to analyze when automatic excision gearing is used. If set to -1 all precursors will be analyzed. (-g)."/> | |
159 <param name="min_score_cutoff" type="integer" value="0" label="Minimum miRNA score" | |
160 help="Minimum score cut-off for predicted novel miRNAs to be displayed in the overview table. (-b)"/> | |
161 <param name="disable_randfold" type="boolean" truevalue="-c" falsevalue="" label="Disable randfold analysis" help="(-c)"/> | |
162 </inputs> | |
163 <outputs> | |
164 <data name="tab_results" format="tabular" from_work_dir="result.csv" label="Tabular output of ${tool.name} on ${on_string}"/> | |
165 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/> | |
166 <data name="pred_acc" format="tabular" from_work_dir="survey.csv" label="Prediction accuracy output of ${tool.name} on ${on_string}"/> | |
167 <data name="bed_out" format="bed" from_work_dir="result.bed" label="Bed output of ${tool.name} on ${on_string}"/> | |
168 <data name="mrd_out" format="txt" from_work_dir="output.mrd" label="Text output of ${tool.name} on ${on_string}"/> | |
169 </outputs> | |
170 <tests> | |
171 <test> | |
172 <param name="reads" value="reads_collapsed.fa"/> | |
173 <param name="genome" value="cel_cluster.fa"/> | |
174 <param name="mappings" value="reads_collapsed_vs_genome.arf"/> | |
175 <param name="mature_this" value="mature_ref_this_species.fa"/> | |
176 <param name="mature_other" value="mature_ref_other_species.fa"/> | |
177 <param name="precursors" value="precursors_ref_this_species.fa"/> | |
178 | |
179 <output name="tab_results" file="result.csv" compare="sim_size"/> | |
180 <output name="prec_acc" file="survey.csv" compare="sim_size"/> | |
181 <output name="bed_out" file="result.bed" compare="sim_size"/> | |
182 <output name="mrd_out" file="output.mrd" compare="sim_size"/> | |
183 </test> | |
184 </tests> | |
185 <help> | |
186 <![CDATA[ | |
187 **What MiRDeep2 does** | |
188 | |
189 MiRDeep2 is a software package for identification of novel and known miRNAs in deep sequencing data. Furthermore, it can be used for miRNA expression profiling across samples. | |
190 ]]> | |
191 </help> | |
192 <citations> | |
193 <citation type="doi">10.1093/nar/gkr688</citation> | |
194 <citation type="doi">10.1002/0471250953.bi1210s36</citation> | |
195 </citations> | |
196 </tool> |