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comparison mirdeep2.xml @ 3:5cecae70d439 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2 commit 3103ebed1a420c7d3415b67ef532ea579edf9faa
author rnateam
date Wed, 12 Jul 2017 14:37:54 -0400
parents b21be04f52e4
children d338dbd76ea0
comparison
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2:d0faf81ccc99 3:5cecae70d439
1 <tool id="rbc_mirdeep2" name="MiRDeep2" version="2.0.0"> 1 <tool id="rbc_mirdeep2" name="MiRDeep2" version="2.0.0">
2 <description> 2 <description>identification of novel and known miRNAs</description>
3 <![CDATA[
4 identification of novel and known miRNAs
5 ]]>
6 </description>
7 <requirements> 3 <requirements>
8 <requirement type="package" version="2.0">mirdeep2</requirement> 4 <requirement type="package" version="2.0.0.8">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> 5 </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 ; mv result*.bed result.bed 2> /dev/null
64 ; mv result*.csv result.csv 2> /dev/null
65 ; mv mirdeep_runs/run*/output.mrd . 2> /dev/null
66 ; mv mirdeep_runs/run*/survey.csv . 2> /dev/null
67
68 ## html output
69 ;
70 mv 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 mv pdfs* $html.files_path 2> /dev/null
77
78 ]]>
79 </command>
80 <stdio> 6 <stdio>
81 <!-- Anything other than zero is an error --> 7 <!-- Anything other than zero is an error -->
82 <exit_code range="1:" /> 8 <exit_code range="1:" />
83 <exit_code range=":-1" /> 9 <exit_code range=":-1" />
84 <!-- In case the return code has not been set propery check stderr too --> 10 <!-- In case the return code has not been set propery check stderr too -->
85 <regex match="Error:" /> 11 <regex match="Error:" />
86 <regex match="Exception:" /> 12 <regex match="Exception:" />
87 </stdio> 13 </stdio>
14 <command>
15 <![CDATA[
16 miRDeep2.pl
17
18 $reads
19 $genome
20 $mappings
21
22 #if $mature_this
23 $mature_this
24 #else
25 none
26 #end if
27
28 #if $mature_other
29 $mature_other
30 #else
31 none
32 #end if
33
34 #if $precursors
35 $precursors
36 #else
37 none
38 #end if
39
40 #if $species.value != 'all'
41 -t $species
42 #end if
43
44 #if $star_sequences
45 -s $star_sequences
46 #end if
47
48 #if $min_read_stack
49 -a $min_read_stack
50 #end if
51
52 #if $min_read_stack
53 -a $min_read_stack
54 #end if
55
56 -g $max_precursors_analyze
57 -b $min_score_cutoff
58 $disable_randfold
59
60 ; mv result*.bed result.bed 2> /dev/null
61 ; mv result*.csv result.csv 2> /dev/null
62 ; mv mirdeep_runs/run*/output.mrd . 2> /dev/null
63 ; mv mirdeep_runs/run*/survey.csv . 2> /dev/null
64
65 ## html output
66 ;
67 mv result*.html $html 2> /dev/null
68
69 ## move pdf directory to be accessible from the new index.html
70 ;
71 mkdir -p $html.files_path 2> /dev/null
72 ;
73 mv pdfs* $html.files_path 2> /dev/null
74
75 ]]>
76 </command>
88 <inputs> 77 <inputs>
89 <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads"> 78 <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads">
90 <help> 79 <help>
91 <![CDATA[ 80 <![CDATA[
92 Reads in fasta format. The identifier should contain a prefix, a running 81 Reads in fasta format. The identifier should contain a prefix, a running
144 <option value="hsa">human</option> 133 <option value="hsa">human</option>
145 <option value="dsi">d.simulans</option> 134 <option value="dsi">d.simulans</option>
146 </param> 135 </param>
147 <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/> 136 <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/>
148 137
149 <param name="min_read_stack" optional="true" type="integer" minvalue="0" label="Minimum read stack height"> 138 <param name="min_read_stack" optional="true" type="integer" min="0" label="Minimum read stack height">
150 <help> 139 <help>
151 <![CDATA[ 140 <![CDATA[
152 minimum read stack height that triggers analysis. Using this option disables 141 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) 142 automatic estimation of the optimal value and all detected precursors are analyzed. (-a)
154 ]]> 143 ]]>
175 <param name="mature_this" value="mature_ref_this_species.fa"/> 164 <param name="mature_this" value="mature_ref_this_species.fa"/>
176 <param name="mature_other" value="mature_ref_other_species.fa"/> 165 <param name="mature_other" value="mature_ref_other_species.fa"/>
177 <param name="precursors" value="precursors_ref_this_species.fa"/> 166 <param name="precursors" value="precursors_ref_this_species.fa"/>
178 167
179 <output name="tab_results" file="result.csv" compare="sim_size"/> 168 <output name="tab_results" file="result.csv" compare="sim_size"/>
180 <output name="prec_acc" file="survey.csv" compare="sim_size"/> 169 <output name="pred_acc" file="survey.csv" compare="sim_size"/>
181 <output name="bed_out" file="result.bed" compare="sim_size"/> 170 <output name="bed_out" file="result.bed" compare="sim_size"/>
182 <output name="mrd_out" file="output.mrd" compare="sim_size"/> 171 <output name="mrd_out" file="output.mrd" compare="sim_size"/>
183 </test> 172 </test>
184 </tests> 173 </tests>
185 <help> 174 <help>
186 <![CDATA[ 175 <![CDATA[
187 **What MiRDeep2 does** 176
177 **What it does**
188 178
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. 179 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.
180
181 **Input**
182
183 A FASTA file with deep sequencing reads, a FASTA file of the corresponding genome, a file of mapped reads to the genome in miRDeep2 arf format, an optional fasta file with known miRNAs of the analysing species and an option fasta file of known miRNAs of related species.
184
185 Arf format:
186 Is a proprietary file format generated and processed by miRDeep2. It contains information of reads mapped to a reference genome. Each line in such a file contains 13 columns:
187
188 1. read identifier
189 2. length of read sequence
190 3. start position in read sequence that is mapped
191 4. end position in read sequence that is mapped
192 5. read sequence
193 6. identifier of the genome-part to which a read is mapped to. This is either a scaffold id or a chromosome name
194 7. length of the genome sequence a read is mapped to
195 8. start position in the genome where a read is mapped to
196 9. end position in the genome where a read is mapped to
197 10. genome sequence to which a read is mapped
198 11. genome strand information. Plus means the read is aligned to the sense-strand of the genome. Minus means it is aligned to the antisense-strand of the genome.
199 12. Number of mismatches in the read mapping
200 13. Edit string that indicates matches by lowercase 'm' and mismatches by uppercase 'M'
201
202
190 ]]> 203 ]]>
191 </help> 204 </help>
192 <citations> 205 <citations>
193 <citation type="doi">10.1093/nar/gkr688</citation> 206 <citation type="doi">10.1093/nar/gkr688</citation>
194 <citation type="doi">10.1002/0471250953.bi1210s36</citation> 207 <citation type="doi">10.1002/0471250953.bi1210s36</citation>