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comparison mirdeep2.xml @ 0:eaac585f172a draft

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author rnateam
date Tue, 27 Jan 2015 09:06:24 -0500
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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>