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>