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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/segemehl commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author rnateam
date Thu, 27 Sep 2018 06:31:11 -0400
parents db367d012fa3
children
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4:db367d012fa3 5:9c0d4ec99ba9
1 <tool id="segemehl" name="segemehl" version="0.2.0.3"> 1 <tool id="segemehl" name="segemehl" version="0.2.0.4">
2 <description>short read mapping with gaps</description> 2 <description>short read mapping with gaps</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="0.2.0">segemehl</requirement> 4 <requirement type="package" version="0.2.0">segemehl</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
8 source="both" 8 source="both"
9 level="fatal" 9 level="fatal"
10 description="Execution halted." /> 10 description="Execution halted." />
11 </stdio> 11 </stdio>
12 <command> 12 <command>
13 <![CDATA[ 13 <!--
14 ## prepare segemehl index if no reference genome is supplied
15 #if $refGenomeSource.genomeSource == "history":
16 mkdir ./temp_index/ &&
17 #set $temp_index = './temp_index/temp.idx'
18 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome &&
19 #else:
20 #set $temp_index = $refGenomeSource.index.fields.index_path
21 #end if
22
23 ## execute segemehl
24 segemehl.x
25
26 ## number of threads
27 -t "\${GALAXY_SLOTS:-12}"
28
29 #if $refGenomeSource.genomeSource == "history":
30 -d $refGenomeSource.own_reference_genome
31 #else:
32 -d ${refGenomeSource.index.fields.db_path}
33 #end if
34
35 -i $temp_index
36
37 ## check for single/pair-end 14 ## check for single/pair-end
38 #if str( $library.type ) == "single": 15 #if str( $library.type ) == "single":
39 #set $query_list = list() 16 #set $query_list = list()
40 ## prepare inputs 17 ## prepare inputs
41 #for $fastq in $library.input_query: 18 #for $fastq in $library.input_query:
54 -q #echo ','.join($mate1) 31 -q #echo ','.join($mate1)
55 -p #echo ','.join($mate2) 32 -p #echo ','.join($mate2)
56 33
57 -I $library.maxinsertsize 34 -I $library.maxinsertsize
58 #end if 35 #end if
36 -->
37 <![CDATA[
38 ## UNIMPLEMENTED
39 ## [SEEDEXTENSIONPARAMS]
40 ## -e, --extensionscore <n> score of a match during extension (default:2)
41 ## -n, --extensionpenalty <n> penalty for a mismatch during extension (default:4)
42 ## -X, --dropoff <n> dropoff parameter for extension (default:8)
43 ## --showalign
44
45 ## prepare segemehl index if no reference genome is supplied
46 #if $refGenomeSource.genomeSource == "history":
47 mkdir ./temp_index/ &&
48 #set $temp_index = './temp_index/temp.idx'
49 segemehl.x -x $temp_index -d $refGenomeSource.own_reference_genome &&
50 #else:
51 #set $temp_index = $refGenomeSource.index.fields.index_path
52 #end if
53
54 ## execute segemehl
55 segemehl.x
56
57 ## number of threads
58 -t "\${GALAXY_SLOTS:-12}"
59
60 #if $refGenomeSource.genomeSource == "history":
61 -d $refGenomeSource.own_reference_genome
62 #else:
63 -d ${refGenomeSource.index.fields.db_path}
64 #end if
65
66 -i $temp_index
67
68 ## check for single/pair-end
69 #if str( $library.type ) == "single":
70 ## prepare inputs
71 -q ${library.input_query}
72 #else
73 -q ${mate_pair.first_strand_query}
74 -p ${mate_pair.second_strand_query}
75 -I ${library.maxinsertsize}
76 #end if
77 #if str( $bisulfite ) != "0":
78 -F $bisulfite
79 #end if
59 -m $minsize 80 -m $minsize
60 -A $accuracy 81 -A $accuracy
61 -H $hitstrategy 82 -H $hitstrategy
62 #if str( $prime5 ).strip(): 83 #if str( $prime5 ).strip():
63 -P "$prime5" 84 -P "$prime5"
64 #end if 85 #end if
65 #if str( $prime3 ).strip(): 86 #if str( $prime3 ).strip():
66 -Q "$prime3" 87 -Q "$prime3"
67 #end if 88 #end if
68 $polyA 89 -R $clipacc
69 $autoclip 90 $polyA
70 $hardclip 91 $autoclip
71 $order 92 $hardclip
93 $order
72 #if $maxout: 94 #if $maxout:
73 --maxout $maxout 95 --maxout $maxout
74 #end if 96 #end if
75 #if str( $splitreads.splits ) == "splits": 97 #if str( $splitreads.splits ) == "splits":
76 --splits 98 --splits
77 --minsplicecover $splitreads.minsplicecover 99 --minsplicecover $splitreads.minsplicecover
78 --minfragscore $splitreads.minfragscore 100 --minfragscore $splitreads.minfragscore
79 --minfraglen $splitreads.minfraglen 101 --minfraglen $splitreads.minfraglen
80 --splicescorescale $splitreads.splicescorescale 102 --splicescorescale $splitreads.splicescorescale
103 --maxsplitevalue $splitreads.maxsplitevalue
81 #end if 104 #end if
82 -M $maxinterval 105 -M $maxinterval
83 -E $evalue 106 -E $evalue
84 -D $differences 107 -D $differences
108 -J $jump
85 -s 109 -s
86 -o '$segemehl_out' 110 -o '$segemehl_out'
111 #if str( $nomatchfilename ) == 'yes':
112 -u '$segemehl_outunmatched'
113 #end if
87 ]]> 114 ]]>
88 </command> 115 </command>
89 <inputs> 116 <inputs>
90 <conditional name="refGenomeSource"> 117 <conditional name="refGenomeSource">
91 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> 118 <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
114 <param name="type" type="select" label="Is this library paired-end?"> 141 <param name="type" type="select" label="Is this library paired-end?">
115 <option value="single">Single-end</option> 142 <option value="single">Single-end</option>
116 <option value="paired">Paired-end</option> 143 <option value="paired">Paired-end</option>
117 </param> 144 </param>
118 <when value="single"> 145 <when value="single">
119 <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" /> 146 <!-- <param name="input_query" type="data" multiple="True" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" /> -->
147 <param name="input_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads in FASTQ/FASTA files" />
120 </when> 148 </when>
121 <when value="paired"> 149 <when value="paired">
122 <!-- ToDo paired coolections --> 150 <!-- ToDo paired coolections -->
123 <repeat name="mate_list" title="Paired End Pairs" min="1"> 151 <repeat name="mate_list" title="Paired End Pairs" min="1">
124 <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" /> 152 <param name="first_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from first strand" />
125 <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" /> 153 <param name="second_strand_query" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="Reads from second strand" />
126 </repeat> 154 </repeat>
127 <param name="maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000 (-I)" /> 155 <param argument="--maxinsertsize" type="integer" value="5000" label="Maximum size of the inserts (paired end)" help="default: 5000" />
128 </when> 156 </when>
129 </conditional> 157 </conditional>
130 158
131 <conditional name="splitreads"> 159 <conditional name="splitreads">
132 <param name="splits" type="select" label="Detect split/spliced reads" help="(--splits)"> 160 <param argument="splits" type="select" label="Detect split/spliced reads">
133 <option value="nosplit">No splits</option> 161 <option value="nosplit">No splits</option>
134 <option value="splits">Split reads</option> 162 <option value="splits">Split reads</option>
135 </param> 163 </param>
136 <when value="splits"> 164 <when value="splits">
137 <param name="minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" help="(--minsplicecover)" /> 165 <param argument="--minsplicecover" type="integer" value="80" label="Min coverage for spliced transcripts" />
138 <param name="minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" help="(--minfragscore)" /> 166 <param argument="--minfragscore" type="integer" value="18" label="Min coverage for spliced transcripts" />
139 <param name="minfraglen" type="integer" value="20" label="Min length of a spliced fragment" help="(--minfraglen)" /> 167 <param argument="--minfraglen" type="integer" value="20" label="Min length of a spliced fragment" />
140 <param name="splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score" 168 <param argument="--splicescorescale" type="float" value="1.0" label="Report spliced alignment with score greater than this scale times the score"
141 help="Report only if this value x score is larger than next best spliced alignment (--splicescorescale)" /> 169 help="Report only if this value x score is larger than next best spliced alignment" />
142 <param name="sevalue" type="float" min="0" value="50.000000" label="max split evalue" help="(--maxsplitevalue)"/> 170 <param argument="--maxsplitevalue" type="float" min="0" value="50.000000" label="max evalue for splits"/>
143 </when> 171 </when>
144 <when value="nosplit"> 172 <when value="nosplit">
145 </when> 173 </when>
146 </conditional> 174 </conditional>
147 175 <param argument="--bisulfite" type="select" label="Bisulfite mapping">
148 <param name="minsize" type="integer" value="12" min="1" label="Minimum size of queries" help="(-m)" /> 176 <option value="0">No bisulfite mapping</option>
149 <param name="maxout" type="integer" min="0" value="0" optional="True" 177 <option value="1">bisulfite mapping with methylC-seq/Lister et al.</option>
150 label="Maximum number of alignments that will be reported" help="(--maxout)" /> 178 <option value="2">bs-seq/Cokus et al. protocol</option>
151 <param name="accuracy" type="integer" value="85" min="1" max="100" label="Min percentage of matches per read in semi-global alignment" help="(-A)" /> 179 </param>
152 <param name="hitstrategy" type="select" label="Hits to report?" help="(-H)"> 180 <param argument="--minsize" type="integer" value="12" min="1" label="Minimum size of queries" />
181 <param argument="--maxout" type="integer" min="0" value="0" optional="True"
182 label="Maximum number of alignments that will be reported"/>
183 <param argument="--accuracy" type="integer" value="85" min="1" max="100" label="Min percentage of matches per read in semi-global alignment" />
184 <param argument="--hitstrategy" type="select" label="Hits to report?">
153 <option value="1">report only best scoring hits</option> 185 <option value="1">report only best scoring hits</option>
154 <option value="0">report all scoring hits</option> 186 <option value="0">report all scoring hits</option>
155 </param> 187 </param>
156 <param name="prime5" type="text" label="add 5' adapter" help="default: none (-Q)" /> 188 <param argument="--prime5" type="text" label="add 5' adapter" help="default: none" />
157 <param name="prime3" type="text" label="add 3' adapter" help="default: none (-P)"/> 189 <param argument="--prime3" type="text" label="add 3' adapter" help="default: none"/>
158 <param name="polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" help="(-T)"/> 190 <param argument="--clipacc" value="70" type="integer" label="clipping accuracy" />
159 <param name="autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter" help="(-Y)"/> 191 <param argument="--polyA" type="boolean" truevalue="--polyA" falsevalue="" checked="false" label="Clip polyA tail" />
160 <param name="hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping" help="(-C)"/> 192 <param argument="--autoclip" type="boolean" truevalue="--autoclip" falsevalue="" checked="false" label="Autoclip unknown 3prime adapter"/>
161 <param name="order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" help="(-O)"/> 193 <param argument="--hardclip" type="boolean" truevalue="--hardclip" falsevalue="" checked="false" label="Enable hard clipping"/>
162 <param name="differences" type="integer" min="0" value="1" label="search seeds initially with n differences" help="(--differences)"/> 194 <param argument="--order" type="boolean" truevalue="--order" falsevalue="" checked="false" label="Sorts the output by chromsome and position" />
163 <param name="evalue" type="float" min="0" value="5.000000" label="max evalue" help="(--evalue)"/> 195 <param argument="--differences" type="integer" min="0" value="1" label="search seeds initially with n differences"/>
164 <param name="maxinterval" type="integer" min="1" value="100" label="maximum width of a suffix array interval, i.e. a query seed will be omitted if it matches more than n times" help="(--maxinterval)"/> 196 <param argument="--jump" type="integer" value="0" min="0" label="search seeds with jump size" help="(0=automatic) (default:0)?"/>
197 <param argument="--evalue" type="float" min="0" value="5.000000" label="max evalue"/>
198 <param argument="--maxinterval" type="integer" min="1" value="100" label="maximum width of a suffix array interval, i.e. a query seed will be omitted if it matches more than n times"/>
199 <param argument="--nomatchfilename" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output unmatched reads"/>
165 </inputs> 200 </inputs>
166 <outputs> 201 <outputs>
167 <data format="sam" name="segemehl_out" label="Read alignments on ${on_string}"/> 202 <data format="sam" name="segemehl_out" label="${tool.name} on ${on_string}"/>
203 <data format="fastq" name="segemehl_outunmatched" label="${tool.name} unaligned reads ${on_string}">
204 <filter>output_unmatched</filter>
205 </data>
168 </outputs> 206 </outputs>
169 <tests> 207 <tests>
170 <test> 208 <test>
171 <param name="genomeSource" value="history" /> 209 <param name="genomeSource" value="history" />
172 <param name="own_reference_genome" value="chr1.fa" /> 210 <param name="own_reference_genome" value="chr1.fa" />
179 <param name="genomeSource" value="history" /> 217 <param name="genomeSource" value="history" />
180 <param name="own_reference_genome" value="chr1.fa" /> 218 <param name="own_reference_genome" value="chr1.fa" />
181 <param name="library" value="single" /> 219 <param name="library" value="single" />
182 <param name="input_query" value="test.fastq" /> 220 <param name="input_query" value="test.fastq" />
183 <param name="splits" value="splits" /> 221 <param name="splits" value="splits" />
184 <param name="minsplicecover" value="40" /> 222 <param name="minsplicecover" value="40" />
223 <param name="nomatchfilename" value="yes" />
185 <output name="segemehl_out" file="testmap2.sam" lines_diff="2" /> 224 <output name="segemehl_out" file="testmap2.sam" lines_diff="2" />
225 <output name="segemehl_outunmatched" file="testmap2.fastq" />
186 </test> 226 </test>
187 </tests> 227 </tests>
188 <help> 228 <help>
189 <![CDATA[ 229 <![CDATA[
190 230