Mercurial > repos > rnateam > mirdeep2_mapper
comparison mapper.xml @ 0:af18bb0baa92 draft
Imported from capsule None
author | rnateam |
---|---|
date | Tue, 27 Jan 2015 09:06:06 -0500 |
parents | |
children | 12fc62b7dc09 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:af18bb0baa92 |
---|---|
1 <tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0"> | |
2 <macros> | |
3 <macro name="map_params"> | |
4 <conditional name="refGenomeSource"> | |
5 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Map to genome. (-p)"> | |
6 <option value="indexed">Use a built-in index</option> | |
7 <option value="history">Use one from the history</option> | |
8 </param> | |
9 <when value="indexed"> | |
10 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin."> | |
11 <options from_data_table="bowtie_indexes"> | |
12 <filter type="sort_by" column="2"/> | |
13 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | |
14 </options> | |
15 </param> | |
16 </when> <!-- build-in --> | |
17 <when value="history"> | |
18 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" /> | |
19 </when> <!-- history --> | |
20 </conditional> <!-- refGenomeSource --> | |
21 <param name="map_mismatch" type="boolean" truevalue="-q" falsevalue="" checked="false" label="Map with one mismatch in the seed (mapping takes longer)" help="(-q)"/> | |
22 <param name="map_threshold" value="5" type="integer" optional="false" label="A read is allowed to map up to this number of positions in the genome" help="Map threshold. (-r)"> | |
23 <validator type="in_range" min="1" message="Minimum value is 1"/> | |
24 </param> | |
25 </macro> | |
26 </macros> | |
27 <description> | |
28 <![CDATA[ | |
29 process and map reads to a reference genome | |
30 ]]> | |
31 </description> | |
32 <requirements> | |
33 <requirement type="package" version="2.0">mirdeep2_mapper</requirement> | |
34 <requirement type="package" version="0.12.7">bowtie</requirement> | |
35 <requirement type="package" version="5.18.1">perl</requirement> | |
36 </requirements> | |
37 | |
38 <command> | |
39 <![CDATA[ | |
40 | |
41 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map" | |
42 #if $operation.refGenomeSource.genomeSource == "history" | |
43 bowtie-build $operation.refGenomeSource.ownFile custom_bowtie_indices && | |
44 #end if | |
45 #end if | |
46 mapper.pl | |
47 | |
48 $reads | |
49 | |
50 #if $reads.extension.startswith("fasta") | |
51 -c | |
52 #else if $reads.extension.startswith("fastq") | |
53 -e -h | |
54 #end if | |
55 | |
56 $remove_non_canon | |
57 | |
58 $convert_rna_dna | |
59 | |
60 #if $clip_adapter.clip == "true" | |
61 -k $clip_adapter.adapter_seq | |
62 #end if | |
63 | |
64 -l $discard_short_reads | |
65 | |
66 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_collapse" | |
67 -m -s $output_reads_collapsed | |
68 #end if | |
69 | |
70 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map" | |
71 -p | |
72 | |
73 #if $operation.refGenomeSource.genomeSource == "history" | |
74 custom_bowtie_indices | |
75 #else | |
76 $index | |
77 #end if | |
78 | |
79 $operation.map_mismatch | |
80 | |
81 -r $operation.map_threshold | |
82 | |
83 -t $output_mapping | |
84 #end if | |
85 | |
86 -v -n | |
87 ]]> | |
88 </command> | |
89 <stdio> | |
90 <!-- Anything other than zero is an error --> | |
91 <exit_code range="1:" /> | |
92 <exit_code range=":-1" /> | |
93 <!-- In case the return code has not been set propery check stderr too --> | |
94 <regex match="Error:" /> | |
95 <regex match="Exception:" /> | |
96 </stdio> | |
97 <inputs> | |
98 <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or fasta format"/> | |
99 <param name="remove_non_canon" type="boolean" truevalue="-j" falsevalue="" checked="false" label="Remove reads with non-standard nucleotides" help="Remove all entries that have a sequence that contains letters other than a,c,g,t,u,n,A,C,G,T,U,N. (-j)"/> | |
100 <param name="convert_rna_dna" type="boolean" truevalue="-i" falsevalue="" checked="false" label="Convert RNA to DNA alphabet (to map against genome)" help="(-i)"/> | |
101 | |
102 <conditional name="clip_adapter"> | |
103 <param name="clip" type="select" label="Clip 3' Adapter Sequence" help="(-k)"> | |
104 <option value="false">Don't Clip</option> | |
105 <option value="true">Clip Sequence</option> | |
106 </param> | |
107 <when value="true"> | |
108 <param name="adapter_seq" value="" type="text" optional="false" label="Sequence to clip" help="Adapter Sequence can only contain a,c,g,t,u,n,A,C,G,T,U,N"> | |
109 <validator type="regex" message="Adapter can ONLY contain a,c,g,t,u,n,A,C,G,T,U,N">^[ACGTUacgtu]+$</validator> | |
110 </param> | |
111 </when> | |
112 <when value="false"/> | |
113 </conditional> | |
114 | |
115 <param name="discard_short_reads" value="18" type="integer" optional="false" label="Discard reads shorter than this length" help="Set to 0 to keep all reads. (-l)"> | |
116 <validator type="in_range" min="0" message="Minimum value is 0"/> | |
117 </param> | |
118 | |
119 <conditional name="operation"> | |
120 <param name="collapse_map" type="select" label="Collapse reads and/or Map" help="(-m) and/or (-p)"> | |
121 <option value="collapse_and_map">Collapse reads and Map</option> | |
122 <option value="only_map">Map</option> | |
123 <option value="only_collapse">Collapse</option> | |
124 </param> | |
125 <when value="collapse_and_map"> | |
126 <expand macro="map_params"/> | |
127 </when> | |
128 <when value="only_map"> | |
129 <expand macro="map_params"/> | |
130 </when> | |
131 <when value="only_collapse"/> | |
132 </conditional> | |
133 </inputs> | |
134 <outputs> | |
135 <data format="fasta" name="output_reads_collapsed" label="Collapsed reads of ${tool.name} on ${on_string}"> | |
136 <filter> | |
137 ( | |
138 operation['collapse_map'] == "collapse_and_map" or | |
139 operation['collapse_map'] == "only_collapse" | |
140 ) | |
141 </filter> | |
142 </data> | |
143 <data format="tabular" name="output_mapping" label="Mapping output of ${tool.name} on ${on_string} in ARF format"> | |
144 <filter> | |
145 ( | |
146 operation['collapse_map'] == "collapse_and_map" or | |
147 operation['collapse_map'] == "only_map" | |
148 ) | |
149 </filter> | |
150 </data> | |
151 </outputs> | |
152 <tests> | |
153 <test> | |
154 <param name="reads" value="reads.fa"/> | |
155 <param name="remove_non_canon" value="True"/> | |
156 <param name="clip" value="true"/> | |
157 <param name="adapter_seq" value="TCGTATGCCGTCTTCTGCTTGT"/> | |
158 <param name="discard_short_reads" value="18"/> | |
159 <param name="collapse_map" value="collapse_and_map"/> | |
160 <param name="genomeSource" value="history"/> | |
161 <param name="ownFile" value="cel_cluster.fa"/> | |
162 <output name="output_reads_collapsed"> | |
163 <assert_contents> | |
164 <has_text text=">seq_349713_x268"/> | |
165 <has_text text="TCACCGGGTGTANATCAGCTAA"/> | |
166 <has_text text=">seq_354255_x214"/> | |
167 <has_text text="TAACCGGGTGAACACTTGCAGT"/> | |
168 <has_text text=">seq_357284_x187"/> | |
169 </assert_contents> | |
170 </output> | |
171 <output name="output_mapping"> | |
172 <assert_contents> | |
173 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagcagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/> | |
174 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagtagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/> | |
175 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtgtacatcagcgaa\tchrII:11534525-11540624\t22\t3631\t3652.*$"/> | |
176 <has_line_matching expression="^.*22\t1\t22\ttcaccgggagaaaaactggtgt\tchrII:11534525-11540624\t22\t3382\t3403.*$"/> | |
177 <has_line_matching expression="^.*25\t1\t25\ttcaccgggtggaaactagcagtggc\tchrII:11534525-11540624\t25\t3060\t3084.*$"/> | |
178 </assert_contents> | |
179 </output> | |
180 </test> | |
181 </tests> | |
182 <help> | |
183 <![CDATA[ | |
184 **What MiRDeep2 Mapper does** | |
185 | |
186 The mapper module is designed as a tool to process deep sequencing reads and/or map them to the reference genome. | |
187 The module works in sequence space, and can process or map data that is in sequence fasta format. | |
188 A number of the functions of the mapper module are implemented specifically with Solexa/Illumina data in mind. | |
189 | |
190 **Example** | |
191 | |
192 Processing reads and mapping them to a genome. | |
193 | |
194 The -c option designates that the input file is a fasta file. The -j options removes entries with | |
195 non-canonical letters (letters other than a,c,g,t,u,n,A,C,G,T,U,N). The -k option clips adapters. The -l option discards reads shorter than 18 nts. | |
196 The -m option collapses the reads. The -p option maps the processed reads against the previously indexed genome (cel_cluster). The -s option | |
197 designates the name of the output file of processed reads and the -t option designates the name of the output file of the genome mappings. Last, | |
198 -v gives verbose output to the screen. | |
199 | |
200 ``mapper.pl reads.fa -c -j -k TCGTATGCCGTCTTCTGCTTGT -l 18 -m -p cel_cluster -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v`` | |
201 | |
202 ]]> | |
203 </help> | |
204 <citations> | |
205 <citation type="doi">10.1093/nar/gkr688</citation> | |
206 <citation type="doi">10.1002/0471250953.bi1210s36</citation> | |
207 </citations> | |
208 </tool> |