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comparison CLIFinder.xml @ 20:f25d12179c6c draft

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"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit d5ec4f62fa3d1d52508e07e1221a0c22f0d615bf"
author clifinder
date Thu, 12 Mar 2020 18:01:10 -0400
parents feecd33c8390
children 7bef1cd4d2ad
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19:5c16e8ddff78 20:f25d12179c6c
1 <tool name="CLIFinder" id="CLIFinder" version="0.5.0" profile="16.01"> 1 <tool name="CLIFinder" id="CLIFinder" version="0.5.1" profile="16.01">
2 <description>Find chimerics transcripts containing LINEs sequences</description> 2 <description>Find chimerics transcripts containing LINEs sequences</description>
3 <macros> 3 <macros>
4 <xml name="source_bwa" token_arg="Argument" token_build="Build argument" token_ref=""> 4 <xml name="source_bwa" token_arg="Argument" token_build="Build argument" token_ref="">
5 <conditional name="source"> 5 <conditional name="source">
6 <param name="source" type="select" label="Will you select the reference database from your history or use a built-in index?"> 6 <param name="source" type="select" label="Will you select the reference database from your history or use a built-in index?">
43 </when> 43 </when>
44 </conditional> 44 </conditional>
45 </xml> 45 </xml>
46 </macros> 46 </macros>
47 <requirements> 47 <requirements>
48 <requirement type="package" version="1.3">seqtk</requirement>
48 <requirement type="package" version="1.9">samtools</requirement> 49 <requirement type="package" version="1.9">samtools</requirement>
49 <requirement type="package" version="2.26.0gx">bedtools</requirement> 50 <requirement type="package" version="2.26.0gx">bedtools</requirement>
50 <requirement type="package" version="4.0.9_p2">repeatmasker</requirement> 51 <requirement type="package" version="4.0.9_p2">repeatmasker</requirement>
51 <requirement type="package" version="0.7.17">bwa</requirement> 52 <requirement type="package" version="0.7.17">bwa</requirement>
52 <requirement type="package" version="0.0.14">fastx_toolkit</requirement> 53 <requirement type="package" version="0.0.14">fastx_toolkit</requirement>
62 </requirements> 63 </requirements>
63 <version_command>perl '$__tool_directory__/script/CLIFinder.pl' --version | head -n 1 | grep 'version' | cut -d ' ' -f 3</version_command> 64 <version_command>perl '$__tool_directory__/script/CLIFinder.pl' --version | head -n 1 | grep 'version' | cut -d ' ' -f 3</version_command>
64 <command detect_errors="aggressive"><![CDATA[ 65 <command detect_errors="aggressive"><![CDATA[
65 perl '$__tool_directory__/script/CLIFinder.pl' 66 perl '$__tool_directory__/script/CLIFinder.pl'
66 67
67 #if str($inputs.custom) == 'true' 68 #if str($inputs.type) == 'paired_collection'
68 #for $x in $inputs.fastq 69 #for $x in $inputs.fastq
69 --first '$x.first' 70 --first '$x.forward'
70 --name '$x.name' 71 --name '$x.name'
71 --second '$x.second' 72 --second '$x.reverse'
72 #end for 73 #end for
73 #else 74 #else
74 #for $x in $inputs.fastq 75 #if str($inputs.datasets.custom_name) == 'true'
75 --first '$x.first' 76 #for $x in $inputs.datasets.fastq
76 --name '$x.first.name' 77 --first '$x.first'
77 --second '$x.second' 78 --name '$x.name'
78 #end for 79 --second '$x.second'
80 #end for
81 #else
82 #for $x in $inputs.datasets.fastq
83 --first '$x.first'
84 --name '$x.first.name'
85 --second '$x.second'
86 #end for
87 #end if
79 #end if 88 #end if
80 89
81 #if $genome.source.source == "history" 90 #if $genome.source.source == "history"
82 --ref '$genome.source.file' 91 --ref '$genome.source.file'
83 --build_ref 92 --build_ref
110 --estdb '$estdb.blast.source.file' 119 --estdb '$estdb.blast.source.file'
111 #end if 120 #end if
112 #if $estdb.blast.source.source == "history" 121 #if $estdb.blast.source.source == "history"
113 --build_estdb 122 --build_estdb
114 #end if 123 #end if
124 #end if
125
126 #if str($species) != ''
127 --species '$species'
115 #end if 128 #end if
116 129
117 --rmsk '$rmsk' 130 --rmsk '$rmsk'
118 --refseq '$refseq' 131 --refseq '$refseq'
119 --html '$chimerae' 132 --html '$chimerae'
127 --threads "\${GALAXY_SLOTS:-4}" 140 --threads "\${GALAXY_SLOTS:-4}"
128 ]]> 141 ]]>
129 </command> 142 </command>
130 <inputs> 143 <inputs>
131 <conditional name="inputs"> 144 <conditional name="inputs">
132 <param name="custom" type="select" label="Use custom name for the input sequence files?"> 145 <param name="type" type="select" label="Input Type">
133 <option value="true">Yes</option> 146 <option value="datasets" selected="true">Distinct datasets</option>
134 <option value="false" selected="true">No: the names will be extracted automatically</option> 147 <option value="paired_collection">Paired collection</option>
135 </param> 148 </param>
136 <when value="true"> 149 <when value="datasets">
137 <repeat name="fastq" title="Input sequences" min="1"> 150 <conditional name="datasets">
138 <param argument="--first" type="data" format="fastqsanger" label="First set of paired-end reads"/> 151 <param name="custom_name" type="select" label="Use custom name for the input sequence files?">
139 <param argument="--name" type="text" value="" label="Label for the input sequences"/> 152 <option value="true">Yes</option>
140 <param argument="--second" type="data" format="fastqsanger" label="Second set of paired-end reads"/> 153 <option value="false" selected="true">No: the names will be extracted automatically</option>
141 </repeat> 154 </param>
155 <when value="true">
156 <repeat name="fastq" title="Input sequences" min="1">
157 <param argument="--first" type="data" format="fastqsanger" label="First set of paired-end reads"/>
158 <param argument="--name" type="text" value="" label="Label for the input sequences"/>
159 <param argument="--second" type="data" format="fastqsanger" label="Second set of paired-end reads"/>
160 </repeat>
161 </when>
162 <when value="false">
163 <repeat name="fastq" title="Input sequences" min="1">
164 <param argument="--first" type="data" format="fastqsanger" label="First set of paired-end reads"/>
165 <param argument="--second" type="data" format="fastqsanger" label="Second set of paired-end reads"/>
166 </repeat>
167 </when>
168 </conditional>
142 </when> 169 </when>
143 <when value="false"> 170 <when value="paired_collection">
144 <repeat name="fastq" title="Input sequences" min="1"> 171 <param name="fastq" format="fastqsanger" type="data_collection" collection_type="list:paired" label="Select paired collection" help="Specify paired dataset collection containing paired reads"/>
145 <param argument="--first" type="data" format="fastqsanger" label="First set of paired-end reads"/>
146 <param argument="--second" type="data" format="fastqsanger" label="Second set of paired-end reads"/>
147 </repeat>
148 </when> 172 </when>
149 </conditional> 173 </conditional>
150 <section name="genome" title="Reference genome" expanded="true"> 174 <section name="genome" title="Reference genome" expanded="true">
151 <expand macro="source_bwa" arg="--ref" build="--build_ref" ref="a reference genome"/> 175 <expand macro="source_bwa" arg="--ref" build="--build_ref" ref="a reference genome"/>
152 </section> 176 </section>
185 <option value="2">TEs sequences in second read in pair</option> 209 <option value="2">TEs sequences in second read in pair</option>
186 </param> 210 </param>
187 <param argument="--size_read" name="size" type="integer" value="100" label="Reads size"/> 211 <param argument="--size_read" name="size" type="integer" value="100" label="Reads size"/>
188 <param argument="--size_insert" name="size_insert" type="integer" value="250" label="Maximum insert size (bp)"/> 212 <param argument="--size_insert" name="size_insert" type="integer" value="250" label="Maximum insert size (bp)"/>
189 <param argument="--min_L1" name="min_L1" type="integer" value="50" label="Minimun bp mapping on selected TEs database"/> 213 <param argument="--min_L1" name="min_L1" type="integer" value="50" label="Minimun bp mapping on selected TEs database"/>
190 <param argument="--mis_L1" name="mis_L1" type="integer" value="2" label="Number of mismatches tolerated in TEs mapping sequences"/> 214 <param argument="--mis_L1" name="mis_L1" type="integer" value="1" label="Number of mismatches tolerated in TEs mapping sequences"/>
191 <param argument="--min_unique" name="min_unique" type="integer" value="33" label="minimum consecutive bp corresponding to a unique sequence"/> 215 <param argument="--min_unique" name="min_unique" type="integer" value="33" label="Minimum consecutive bp corresponding to a unique sequence"/>
216 <param argument="--species" name="species" type="text" value="human" label="Species or clade of the input sequence (the species name must be a valid NCBI Taxonomy Database species name and be contained in the RepeatMasker repeat database)"/>
192 </inputs> 217 </inputs>
193 <outputs> 218 <outputs>
194 <data format="html" name="chimerae" label="${tool.name}_on_${on_string}"/> 219 <data format="html" name="chimerae" label="${tool.name}_on_${on_string}"/>
195 </outputs> 220 </outputs>
196 <tests> 221 <tests>
197 <test> 222 <test>
198 <conditional name="inputs"> 223 <conditional name="inputs">
199 <param name="custom" value="true"/> 224 <param name="type" value="datasets"/>
200 <repeat name="fastq"> 225 <conditional name="datasets">
201 <param name="first" value="one.fastq" ftype="fastqsanger" /> 226 <param name="custom_name" value="true"/>
202 <param name="name" value="test"/> 227 <repeat name="fastq">
203 <param name="second" value="two.fastq" ftype="fastqsanger" /> 228 <param name="first" value="one.fastq" ftype="fastqsanger" />
204 </repeat> 229 <param name="name" value="test"/>
230 <param name="second" value="two.fastq" ftype="fastqsanger" />
231 </repeat>
232 </conditional>
205 </conditional> 233 </conditional>
206 <section name="genome"> 234 <section name="genome">
207 <conditional name="source"> 235 <conditional name="source">
208 <param name="source" value="history" /> 236 <param name="source" value="history" />
209 <param name="file" value ="genome.fa" /> 237 <param name="file" value ="genome.fa" />
248 </output> 276 </output>
249 </test> 277 </test>
250 </tests> 278 </tests>
251 <help> 279 <help>
252 <![CDATA[ 280 <![CDATA[
253 **CLIFinder version 0.5.0**
254
255 **Usage:** 281 **Usage:**
256 282
257 CLIFinder.pl --first [first fastq of paired-end set 1] --name [name 1] --second [second fastq of paired-end set 1] [--first [first fastq of paired-end set 2] --name [name 2] --second [second fastq of paired-end set 2] ...] --ref [reference genome] [--build_ref] --TE [transposable elements] [--build_TE] --html [results.html] --html-path [results directory][options] 283 `CLIFinder.pl --first <first fastq of paired-end set 1> --name <name 1> --second <second fastq of paired-end set 1> [--first <first fastq of paired-end set 2> --name <name 2> --second <second fastq of paired-end set 2> ...] --ref <reference genome> [--build_ref] --TE <transposable elements> [--build_TE] --html <results.html> --html-path <results directory> [options]`
258 284
259 **Arguments:** 285 **Arguments:**
260 --first [fastq] First fastq file to process from paired-end set 286 --first First fastq file to process from paired-end set
261 287 --name Name of the content to process
262 --name [name] Name of the content to process 288 --second Second fastq file to process from paired-end set
263 289 --ref Fasta file containing the reference genome
264 --second [fastq] Second fastq file to process from paired-end set 290 --TE Fasta file containing the transposable elements
265 291 --rmsk Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC)
266 --ref [reference] Fasta file containing the reference genome 292 --refseq Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC)
267 293 --html Main HTML file where results will be displayed
268 --TE [TE] Fasta file containing the transposable elements 294 --html-path Folder where results will be stored
269
270 --rmsk [txt file] Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC)
271
272 --refseq [txt file] Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC)
273
274 --html [file] Main HTML file where results will be displayed
275
276 --html-path [path] Folder where results will be stored
277 295
278 For any fasta file, if a bwa index is not provided, you should build it through the corresponding *--build_[element]* argument 296 For any fasta file, if a bwa index is not provided, you should build it through the corresponding *--build_[element]* argument
279 297
280 **Options:** 298 **Options:**
281 --rnadb [RNA db] Blast database with RNA sequences (optional) 299 --rnadb Blast database with RNA sequences (optional)
282 300 --estdb Blast database with RNA sequences (optional)
283 --estdb [EST db] Blast database with RNA sequences (optional) 301 --size_read Size of reads (default: 100)
284 302 --BDir Orientation of reads (0: undirectional libraries, 1: TEs sequences in first read in pair, 2: TEs sequences in second read in pair)
285 --size_read [INT] Size of reads 303 --size_insert Maximum size of insert tolerated between R1 and R2 for alignment on the reference genome (default: 250)
286 304 --min_L1 Minimum number of bp matching for L1 mapping (default: 50)
287 --BDir [0|1|2] Orientation of reads (0: undirectional libraries, 1: TEs sequences in first read in pair, 2: TEs sequences in second read in pair) 305 --mis_L1 Maximum number of mismatches tolerated for L1 mapping (default: 1)
288 306 --min_unique Number of consecutive bp not annotated by RepeatMasker (default: 33)
289 --size_insert [INT] Maximum size of insert tolerated between R1 and R2 for alignment on the reference genome 307 --species Species to use in RepeatMasker (default: human)
290 308 --threads Number of threads (default: 1)
291 --min_L1 [INT] Minimum number of bp matching for L1 mapping
292
293 --mis_L1 [INT] Maximum number of mismatches tolerated for L1 mapping
294
295 --min_unique [INT] Number of consecutive bp not annotated by RepeatMasker
296
297 --threads [INT] Number of threads (default: 1)
298 309
299 For Blast database files, if a fasta is provided, the database can be built with '--build_[db]'. Otherwise, provide a path or URL. "tar(.gz)" files are acceptable, as well as wild card (rna*) URLs. 310 For Blast database files, if a fasta is provided, the database can be built with '--build_[db]'. Otherwise, provide a path or URL. "tar(.gz)" files are acceptable, as well as wild card (rna*) URLs.
300 311
301 ]]> 312 ]]>
302 </help> 313 </help>