annotate mapper.xml @ 1:12fc62b7dc09 draft

Uploaded
author rnateam
date Thu, 12 Feb 2015 09:46:55 -0500
parents af18bb0baa92
children ab8cd78709e1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
1 <tool id="rbc_mirdeep2_mapper" name="MiRDeep2 Mapper" version="2.0.0">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
2 <macros>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
3 <macro name="map_params">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
4 <conditional name="refGenomeSource">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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)">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
6 <option value="indexed">Use a built-in index</option>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
7 <option value="history">Use one from the history</option>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
8 </param>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
9 <when value="indexed">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
10 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin.">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
11 <options from_data_table="bowtie_indexes">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
12 <filter type="sort_by" column="2"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
13 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
14 </options>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
15 </param>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
16 </when> <!-- build-in -->
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
17 <when value="history">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
18 <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
19 </when> <!-- history -->
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
20 </conditional> <!-- refGenomeSource -->
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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)"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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)">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
23 <validator type="in_range" min="1" message="Minimum value is 1"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
24 </param>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
25 </macro>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
26 </macros>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
27 <description>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
28 <![CDATA[
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
29 process and map reads to a reference genome
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
30 ]]>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
31 </description>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
32 <requirements>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
33 <requirement type="package" version="2.0">mirdeep2_mapper</requirement>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
34 <requirement type="package" version="0.12.7">bowtie</requirement>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
35 <requirement type="package" version="5.18.1">perl</requirement>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
36 </requirements>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
37
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
38 <command>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
39 <![CDATA[
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
40
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
41 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
42 #if $operation.refGenomeSource.genomeSource == "history"
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
43 bowtie-build $operation.refGenomeSource.ownFile custom_bowtie_indices &&
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
44 #end if
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
45 #end if
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
46 mapper.pl
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
47
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
48 $reads
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
49
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
50 #if $reads.extension.startswith("fasta")
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
51 -c
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
52 #else if $reads.extension.startswith("fastq")
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
53 -e -h
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
54 #end if
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
55
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
56 $remove_non_canon
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
57
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
58 $convert_rna_dna
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
59
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
60 #if $clip_adapter.clip == "true"
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
61 -k $clip_adapter.adapter_seq
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
62 #end if
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
63
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
64 -l $discard_short_reads
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
65
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
66 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_collapse"
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
67 -m -s $output_reads_collapsed
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
68 #end if
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
69
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
70 #if $operation.collapse_map == "collapse_and_map" or $operation.collapse_map == "only_map"
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
71 -p
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
72
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
73 #if $operation.refGenomeSource.genomeSource == "history"
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
74 custom_bowtie_indices
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
75 #else
1
12fc62b7dc09 Uploaded
rnateam
parents: 0
diff changeset
76 $operation.refGenomeSource.index
0
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
77 #end if
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
78
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
79 $operation.map_mismatch
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
80
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
81 -r $operation.map_threshold
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
82
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
83 -t $output_mapping
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
84 #end if
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
85
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
86 -v -n
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
87 ]]>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
88 </command>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
89 <stdio>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
90 <!-- Anything other than zero is an error -->
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
91 <exit_code range="1:" />
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
92 <exit_code range=":-1" />
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
93 <!-- In case the return code has not been set propery check stderr too -->
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
94 <regex match="Error:" />
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
95 <regex match="Exception:" />
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
96 </stdio>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
97 <inputs>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
98 <param format="fastq, fasta" name="reads" type="data" optional="false" label="Deep sequencing reads" help="Reads in fastq or fasta format"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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)"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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)"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
101
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
102 <conditional name="clip_adapter">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
103 <param name="clip" type="select" label="Clip 3' Adapter Sequence" help="(-k)">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
104 <option value="false">Don't Clip</option>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
105 <option value="true">Clip Sequence</option>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
106 </param>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
107 <when value="true">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
109 <validator type="regex" message="Adapter can ONLY contain a,c,g,t,u,n,A,C,G,T,U,N">^[ACGTUacgtu]+$</validator>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
110 </param>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
111 </when>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
112 <when value="false"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
113 </conditional>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
114
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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)">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
116 <validator type="in_range" min="0" message="Minimum value is 0"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
117 </param>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
118
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
119 <conditional name="operation">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
120 <param name="collapse_map" type="select" label="Collapse reads and/or Map" help="(-m) and/or (-p)">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
121 <option value="collapse_and_map">Collapse reads and Map</option>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
122 <option value="only_map">Map</option>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
123 <option value="only_collapse">Collapse</option>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
124 </param>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
125 <when value="collapse_and_map">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
126 <expand macro="map_params"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
127 </when>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
128 <when value="only_map">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
129 <expand macro="map_params"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
130 </when>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
131 <when value="only_collapse"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
132 </conditional>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
133 </inputs>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
134 <outputs>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
135 <data format="fasta" name="output_reads_collapsed" label="Collapsed reads of ${tool.name} on ${on_string}">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
136 <filter>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
137 (
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
138 operation['collapse_map'] == "collapse_and_map" or
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
139 operation['collapse_map'] == "only_collapse"
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
140 )
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
141 </filter>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
142 </data>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
143 <data format="tabular" name="output_mapping" label="Mapping output of ${tool.name} on ${on_string} in ARF format">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
144 <filter>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
145 (
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
146 operation['collapse_map'] == "collapse_and_map" or
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
147 operation['collapse_map'] == "only_map"
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
148 )
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
149 </filter>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
150 </data>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
151 </outputs>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
152 <tests>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
153 <test>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
154 <param name="reads" value="reads.fa"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
155 <param name="remove_non_canon" value="True"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
156 <param name="clip" value="true"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
157 <param name="adapter_seq" value="TCGTATGCCGTCTTCTGCTTGT"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
158 <param name="discard_short_reads" value="18"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
159 <param name="collapse_map" value="collapse_and_map"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
160 <param name="genomeSource" value="history"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
161 <param name="ownFile" value="cel_cluster.fa"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
162 <output name="output_reads_collapsed">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
163 <assert_contents>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
164 <has_text text=">seq_349713_x268"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
165 <has_text text="TCACCGGGTGTANATCAGCTAA"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
166 <has_text text=">seq_354255_x214"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
167 <has_text text="TAACCGGGTGAACACTTGCAGT"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
168 <has_text text=">seq_357284_x187"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
169 </assert_contents>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
170 </output>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
171 <output name="output_mapping">
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
172 <assert_contents>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
173 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagcagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
174 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtggaaactagtagt\tchrII:11534525-11540624\t22\t3060\t3081.*$"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
175 <has_line_matching expression="^.*22\t1\t22\ttcaccgggtgtacatcagcgaa\tchrII:11534525-11540624\t22\t3631\t3652.*$"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
176 <has_line_matching expression="^.*22\t1\t22\ttcaccgggagaaaaactggtgt\tchrII:11534525-11540624\t22\t3382\t3403.*$"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
177 <has_line_matching expression="^.*25\t1\t25\ttcaccgggtggaaactagcagtggc\tchrII:11534525-11540624\t25\t3060\t3084.*$"/>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
178 </assert_contents>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
179 </output>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
180 </test>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
181 </tests>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
182 <help>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
183 <![CDATA[
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
184 **What MiRDeep2 Mapper does**
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
185
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
186 The mapper module is designed as a tool to process deep sequencing reads and/or map them to the reference genome.
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
187 The module works in sequence space, and can process or map data that is in sequence fasta format.
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
188 A number of the functions of the mapper module are implemented specifically with Solexa/Illumina data in mind.
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
189
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
190 **Example**
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
191
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
192 Processing reads and mapping them to a genome.
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
193
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
194 The -c option designates that the input file is a fasta file. The -j options removes entries with
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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.
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
196 The -m option collapses the reads. The -p option maps the processed reads against the previously indexed genome (cel_cluster). The -s option
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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,
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
198 -v gives verbose output to the screen.
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
199
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
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``
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
201
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
202 ]]>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
203 </help>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
204 <citations>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
205 <citation type="doi">10.1093/nar/gkr688</citation>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
206 <citation type="doi">10.1002/0471250953.bi1210s36</citation>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
207 </citations>
af18bb0baa92 Imported from capsule None
rnateam
parents:
diff changeset
208 </tool>