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comparison mirdeep2.xml @ 4:d338dbd76ea0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/mirdeep2/mirdeep2 commit 04c75332ac618b43ce5c3f307f7866e97147e865
author rnateam
date Thu, 05 Apr 2018 08:37:10 -0400
parents 5cecae70d439
children 6a17e1229b9f
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3:5cecae70d439 4:d338dbd76ea0
1 <tool id="rbc_mirdeep2" name="MiRDeep2" version="2.0.0"> 1 <tool id="rbc_mirdeep2" name="MiRDeep2" version="2.0.0.8.1">
2 <description>identification of novel and known miRNAs</description> 2 <description>identification of novel and known miRNAs</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.0.0.8">mirdeep2</requirement> 4 <requirement type="package" version="2.0.0.8">mirdeep2</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <command detect_errors="aggressive">
7 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 <!-- In case the return code has not been set propery check stderr too -->
11 <regex match="Error:" />
12 <regex match="Exception:" />
13 </stdio>
14 <command>
15 <![CDATA[ 7 <![CDATA[
16 miRDeep2.pl 8 miRDeep2.pl
17 9
18 $reads 10 $reads
19 $genome 11 $genome
20 $mappings 12 $mappings
21 13
22 #if $mature_this 14 #if $mature_this
23 $mature_this 15 $mature_this
24 #else 16 #else
25 none 17 none
26 #end if 18 #end if
27 19
28 #if $mature_other 20 #if $mature_other
29 $mature_other 21 $mature_other
30 #else 22 #else
31 none 23 none
32 #end if 24 #end if
33 25
34 #if $precursors 26 #if $precursors
35 $precursors 27 $precursors
36 #else 28 #else
37 none 29 none
38 #end if 30 #end if
39 31
40 #if $species.value != 'all' 32 #if $species.value != 'all'
41 -t $species 33 -t $species
42 #end if 34 #end if
43 35
44 #if $star_sequences 36 #if $star_sequences
45 -s $star_sequences 37 -s $star_sequences
46 #end if 38 #end if
47 39
48 #if $min_read_stack 40 #if $min_read_stack
49 -a $min_read_stack 41 -a $min_read_stack
50 #end if 42 #end if
51 43
52 #if $min_read_stack 44 #if $min_read_stack
53 -a $min_read_stack 45 -a $min_read_stack
54 #end if 46 #end if
55 47
56 -g $max_precursors_analyze 48 -g $max_precursors_analyze
57 -b $min_score_cutoff 49 -b $min_score_cutoff
58 $disable_randfold 50 $disable_randfold
59 51
60 ; mv result*.bed result.bed 2> /dev/null 52 &&
61 ; mv result*.csv result.csv 2> /dev/null 53
62 ; mv mirdeep_runs/run*/output.mrd . 2> /dev/null
63 ; mv mirdeep_runs/run*/survey.csv . 2> /dev/null
64
65 ## html output 54 ## html output
66 ;
67 mv result*.html $html 2> /dev/null 55 mv result*.html $html 2> /dev/null
68 56
69 ## move pdf directory to be accessible from the new index.html 57 ## move pdf directory to be accessible from the new index.html
70 ; 58 &&
71 mkdir -p $html.files_path 2> /dev/null 59 mkdir -p $html.files_path 2> /dev/null
72 ; 60 &&
73 mv pdfs* $html.files_path 2> /dev/null 61 mv pdfs* $html.files_path 2> /dev/null
74
75 ]]> 62 ]]>
76 </command> 63 </command>
77 <inputs> 64 <inputs>
78 <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads"> 65 <param name="reads" format="fasta" type="data" label="Collapsed deep sequencing reads">
79 <help> 66 <help>
80 <![CDATA[ 67 <![CDATA[
81 Reads in fasta format. The identifier should contain a prefix, a running 68 Reads in fasta format. The identifier should contain a prefix, a running
82 number and a '_x' to indicate the number of reads that have this sequence. 69 number and a '_x' to indicate the number of reads that have this sequence.
84 ]]> 71 ]]>
85 </help> 72 </help>
86 </param> 73 </param>
87 <param name="genome" format="fasta" type="data" label="Genome" help="Genome contigs in fasta format. The identifiers should be unique."/> 74 <param name="genome" format="fasta" type="data" label="Genome" help="Genome contigs in fasta format. The identifiers should be unique."/>
88 <param name="mappings" format="tabular" type="data" label="Mappings" help="Reads mapped against genome. Mappings should be in ARF format."/> 75 <param name="mappings" format="tabular" type="data" label="Mappings" help="Reads mapped against genome. Mappings should be in ARF format."/>
89 <param name="mature_this" optional="true" format="fasta" type="data" label="Mature miRNA sequences for this species" 76 <param name="mature_this" optional="true" format="fasta" type="data" label="Mature miRNA sequences for this species"
90 help="miRBase miRNA sequences in fasta format. These should be the known mature sequences for the species being analyzed."/> 77 help="miRBase miRNA sequences in fasta format. These should be the known mature sequences for the species being analyzed."/>
91 <param name="mature_other" optional="true" format="fasta" type="data" label="Mature miRNA sequences for related species"> 78 <param name="mature_other" optional="true" format="fasta" type="data" label="Mature miRNA sequences for related species">
92 <help> 79 <help>
93 <![CDATA[ 80 <![CDATA[
94 miRBase miRNA sequences in fasta format. These should be the pooled known 81 miRBase miRNA sequences in fasta format. These should be the pooled known
95 mature sequences for 1-5 species closely related to the species being analyzed. 82 mature sequences for 1-5 species closely related to the species being analyzed.
96 ]]> 83 ]]>
97 </help> 84 </help>
98 </param> 85 </param>
99 <param name="precursors" optional="true" format="fasta" type="data" label="Precursor sequences" 86 <param name="precursors" optional="true" format="fasta" type="data" label="Precursor sequences"
100 help="miRBase miRNA precursor sequences in fasta format. These should be the known precursor sequences for the species being analyzed."/> 87 help="miRBase miRNA precursor sequences in fasta format. These should be the known precursor sequences for the species being analyzed."/>
101 88
102 <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)"> 89 <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)">
103 <option value="all">All species</option> 90 <option value="all">All species</option>
104 <option value="tni">tetraodon</option> 91 <option value="tni">tetraodon</option>
105 <option value="dps">d.pseudoobscura</option> 92 <option value="dps">d.pseudoobscura</option>
106 <option value="dya">d.yakuba</option> 93 <option value="dya">d.yakuba</option>
132 <option value="dan">d.ananassae</option> 119 <option value="dan">d.ananassae</option>
133 <option value="hsa">human</option> 120 <option value="hsa">human</option>
134 <option value="dsi">d.simulans</option> 121 <option value="dsi">d.simulans</option>
135 </param> 122 </param>
136 <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/> 123 <param name="star_sequences" format="fasta" type="data" optional="true" label="Star sequences" help="From miRBase in fasta format (optional) (-s)"/>
137 124
138 <param name="min_read_stack" optional="true" type="integer" min="0" label="Minimum read stack height"> 125 <param name="min_read_stack" optional="true" type="integer" min="0" label="Minimum read stack height">
139 <help> 126 <help>
140 <![CDATA[ 127 <![CDATA[
141 minimum read stack height that triggers analysis. Using this option disables 128 minimum read stack height that triggers analysis. Using this option disables
142 automatic estimation of the optimal value and all detected precursors are analyzed. (-a) 129 automatic estimation of the optimal value and all detected precursors are analyzed. (-a)
143 ]]> 130 ]]>
144 </help> 131 </help>
145 </param> 132 </param>
146 <param name="max_precursors_analyze" type="integer" value="50000" label="Maximum precursors" 133 <param name="max_precursors_analyze" type="integer" value="50000" label="Maximum precursors"
147 help="Maximum number of precursors to analyze when automatic excision gearing is used. If set to -1 all precursors will be analyzed. (-g)."/> 134 help="Maximum number of precursors to analyze when automatic excision gearing is used. If set to -1 all precursors will be analyzed. (-g)."/>
148 <param name="min_score_cutoff" type="integer" value="0" label="Minimum miRNA score" 135 <param name="min_score_cutoff" type="integer" value="0" label="Minimum miRNA score"
149 help="Minimum score cut-off for predicted novel miRNAs to be displayed in the overview table. (-b)"/> 136 help="Minimum score cut-off for predicted novel miRNAs to be displayed in the overview table. (-b)"/>
150 <param name="disable_randfold" type="boolean" truevalue="-c" falsevalue="" label="Disable randfold analysis" help="(-c)"/> 137 <param name="disable_randfold" type="boolean" truevalue="-c" falsevalue="" label="Disable randfold analysis" help="(-c)"/>
138 <param name="detailed_fasta" type="boolean" checked="false" label="Detailed fasta output" help="Output fasta files of precursors, mature and star strand for both novel and known miRNAs"/>
151 </inputs> 139 </inputs>
152 <outputs> 140 <outputs>
153 <data name="tab_results" format="tabular" from_work_dir="result.csv" label="Tabular output of ${tool.name} on ${on_string}"/> 141 <data name="tab_results" format="tabular" from_work_dir="result*.csv" label="Tabular output of ${tool.name} on ${on_string}"/>
154 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/> 142 <data format="html" name="html" label="${tool.name} on ${on_string} (html report)"/>
155 <data name="pred_acc" format="tabular" from_work_dir="survey.csv" label="Prediction accuracy output of ${tool.name} on ${on_string}"/> 143 <data name="pred_acc" format="tabular" from_work_dir="mirdeep_runs/run*/survey.csv" label="Prediction accuracy output of ${tool.name} on ${on_string}"/>
156 <data name="bed_out" format="bed" from_work_dir="result.bed" label="Bed output of ${tool.name} on ${on_string}"/> 144 <data name="bed_out" format="bed" from_work_dir="result*.bed" label="Bed output of ${tool.name} on ${on_string}"/>
157 <data name="mrd_out" format="txt" from_work_dir="output.mrd" label="Text output of ${tool.name} on ${on_string}"/> 145 <data name="mrd_out" format="txt" from_work_dir="mirdeep_runs/run*/output.mrd" label="Text output of ${tool.name} on ${on_string}"/>
146
147 <data name="known_mature" format="fasta" from_work_dir="mirna_results_*/known_mature_*.fa" label="${tool.name} on ${on_string}: known mature">
148 <filter>detailed_fasta</filter>
149 </data>
150 <data name="known_pres" format="fasta" from_work_dir="mirna_results_*/known_pres_*.fa" label="${tool.name} on ${on_string}: known precursors">
151 <filter>detailed_fasta</filter>
152 </data>
153 <data name="known_star" format="fasta" from_work_dir="mirna_results_*/known_star_*.fa" label="${tool.name} on ${on_string}: known star">
154 <filter>detailed_fasta</filter>
155 </data>
156 <data name="not_mature" format="fasta" from_work_dir="mirna_results_*/not_mature_*.fa" label="${tool.name} on ${on_string}: not detected mature">
157 <filter>detailed_fasta</filter>
158 </data>
159 <data name="not_pres" format="fasta" from_work_dir="mirna_results_*/not_pres_*.fa" label="${tool.name} on ${on_string}: not detected precursors">
160 <filter>detailed_fasta</filter>
161 </data>
162 <data name="not_star" format="fasta" from_work_dir="mirna_results_*/not_star_*.fa" label="${tool.name} on ${on_string}: not detected star">
163 <filter>detailed_fasta</filter>
164 </data>
165 <data name="novel_mature" format="fasta" from_work_dir="mirna_results_*/novel_mature_*.fa" label="${tool.name} on ${on_string}: novel mature">
166 <filter>detailed_fasta</filter>
167 </data>
168 <data name="novel_pres" format="fasta" from_work_dir="mirna_results_*/novel_pres_*.fa" label="${tool.name} on ${on_string}: novel precursors">
169 <filter>detailed_fasta</filter>
170 </data>
171 <data name="novel_star" format="fasta" from_work_dir="mirna_results_*/novel_star_*.fa" label="${tool.name} on ${on_string}: novel star">
172 <filter>detailed_fasta</filter>
173 </data>
158 </outputs> 174 </outputs>
159 <tests> 175 <tests>
160 <test> 176 <test>
161 <param name="reads" value="reads_collapsed.fa"/> 177 <param name="reads" value="reads_collapsed.fa"/>
162 <param name="genome" value="cel_cluster.fa"/> 178 <param name="genome" value="cel_cluster.fa"/>
163 <param name="mappings" value="reads_collapsed_vs_genome.arf"/> 179 <param name="mappings" value="reads_collapsed_vs_genome.arf"/>
164 <param name="mature_this" value="mature_ref_this_species.fa"/> 180 <param name="mature_this" value="mature_ref_this_species.fa"/>
165 <param name="mature_other" value="mature_ref_other_species.fa"/> 181 <param name="mature_other" value="mature_ref_other_species.fa"/>
166 <param name="precursors" value="precursors_ref_this_species.fa"/> 182 <param name="precursors" value="precursors_ref_this_species.fa"/>
167 183
168 <output name="tab_results" file="result.csv" compare="sim_size"/> 184 <output name="tab_results" file="result.csv" compare="sim_size"/>
169 <output name="pred_acc" file="survey.csv" compare="sim_size"/> 185 <output name="pred_acc" file="survey.csv" compare="sim_size"/>
170 <output name="bed_out" file="result.bed" compare="sim_size"/> 186 <output name="bed_out" file="result.bed" compare="sim_size"/>
171 <output name="mrd_out" file="output.mrd" compare="sim_size"/> 187 <output name="mrd_out" file="output.mrd" compare="sim_size"/>
188 </test>
189 <test>
190 <param name="reads" value="reads_collapsed.fa"/>
191 <param name="genome" value="cel_cluster.fa"/>
192 <param name="mappings" value="reads_collapsed_vs_genome.arf"/>
193 <param name="mature_this" value="mature_ref_this_species.fa"/>
194 <param name="mature_other" value="mature_ref_other_species.fa"/>
195 <param name="precursors" value="precursors_ref_this_species.fa"/>
196 <param name="detailed_fasta" value="true"/>
197
198 <output name="tab_results" file="result.csv" compare="sim_size"/>
199 <output name="pred_acc" file="survey.csv" compare="sim_size"/>
200 <output name="bed_out" file="result.bed" compare="sim_size"/>
201 <output name="mrd_out" file="output.mrd" compare="sim_size"/>
202
203 <output name="known_mature" file="detailed_fasta/known_mature.fa" compare="sim_size"/>
204 <output name="known_pres" file="detailed_fasta/known_pres.fa" compare="sim_size"/>
205 <output name="known_star" file="detailed_fasta/known_star.fa" compare="sim_size"/>
206 <output name="not_mature" file="detailed_fasta/not_mature.fa" compare="sim_size"/>
207 <output name="not_pres" file="detailed_fasta/not_pres.fa" compare="sim_size"/>
208 <output name="not_star" file="detailed_fasta/not_star.fa" compare="sim_size"/>
209 <output name="novel_mature" file="detailed_fasta/novel_mature.fa" compare="sim_size"/>
210 <output name="novel_pres" file="detailed_fasta/novel_pres.fa" compare="sim_size"/>
211 <output name="novel_star" file="detailed_fasta/novel_star.fa" compare="sim_size"/>
172 </test> 212 </test>
173 </tests> 213 </tests>
174 <help> 214 <help>
175 <![CDATA[ 215 <![CDATA[
176 216