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comparison pal_finder_wrapper.xml @ 12:d26fb5260c67 draft

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0.02.04.6: update to use conda to resolve dependencies.
author pjbriggs
date Thu, 15 Mar 2018 09:49:05 -0400
parents 84613d5f1713
children 3f8bf1a0403b
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11:84613d5f1713 12:d26fb5260c67
1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.6"> 1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.6">
2 <description>Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them</description> 2 <description>Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them</description>
3 <macros>
4 <import>pal_finder_macros.xml</import>
5 </macros>
3 <requirements> 6 <requirements>
4 <requirement type="package" version="5.16.3">perl</requirement>
5 <requirement type="package" version="0.02.04">pal_finder</requirement> 7 <requirement type="package" version="0.02.04">pal_finder</requirement>
6 <requirement type="package" version="2.0.0">primer3_core</requirement> 8 <requirement type="package" version="2.7">python</requirement>
7 <requirement type="package" version="1.65">biopython</requirement> 9 <requirement type="package" version="1.65">biopython</requirement>
8 <requirement type="package" version="2.8.1">pandaseq</requirement> 10 <requirement type="package" version="2.8.1">pandaseq</requirement>
9 </requirements> 11 </requirements>
10 <command interpreter="bash">pal_finder_wrapper.sh 12 <command><![CDATA[
13 @CONDA_PAL_FINDER_SCRIPT_DIR@ &&
14 @CONDA_PAL_FINDER_DATA_DIR@ &&
15 bash $__tool_directory__/pal_finder_wrapper.sh
11 #if str( $platform.platform_type ) == "illumina" 16 #if str( $platform.platform_type ) == "illumina"
12 #set $paired_input_type = $platform.paired_input_type_conditional.paired_input_type 17 #set $paired_input_type = $platform.paired_input_type_conditional.paired_input_type
13 #if $paired_input_type == "pair_of_files" 18 #if $paired_input_type == "pair_of_files"
14 "$platform.paired_input_type_conditional.input_fastq_r1" 19 "$platform.paired_input_type_conditional.input_fastq_r1"
15 "$platform.paired_input_type_conditional.input_fastq_r2" 20 "$platform.paired_input_type_conditional.input_fastq_r2"
55 #end if 60 #end if
56 #if str( $platform.assembly ) == '-assembly' 61 #if str( $platform.assembly ) == '-assembly'
57 $platform.assembly "$output_assembly" 62 $platform.assembly "$output_assembly"
58 #end if 63 #end if
59 #end if 64 #end if
60 </command> 65 ]]></command>
61 <inputs> 66 <inputs>
62 <param name="primer_prefix" type="text" value="test" size="25" label="Primer prefix" help="This prefix will be added to the beginning of all primer names" /> 67 <param name="primer_prefix" type="text" value="test" size="25" label="Primer prefix" help="This prefix will be added to the beginning of all primer names" />
63 <conditional name="platform"> 68 <conditional name="platform">
64 <param name="platform_type" type="select" label="Sequencing platform used to generate data" help="Currently pal_finder only handles Illumina paired-end reads and 454 single-end reads" > 69 <param name="platform_type" type="select" label="Sequencing platform used to generate data" help="Currently pal_finder only handles Illumina paired-end reads and 454 single-end reads" >
65 <option value="illumina" selected="true">Illumina</option> 70 <option value="illumina" selected="true">Illumina</option>
167 <data name="output_config_file" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: config file"> 172 <data name="output_config_file" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: config file">
168 <filter>keep_config_file is True</filter> 173 <filter>keep_config_file is True</filter>
169 </data> 174 </data>
170 </outputs> 175 </outputs>
171 <tests> 176 <tests>
172 <test> 177 <!-- Test with Illumina input -->
173 <!-- Test with Illumina input --> 178 <test>
174 <param name="platform_type" value="illumina" /> 179 <param name="platform_type" value="illumina" />
175 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> 180 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
176 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> 181 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
177 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> 182 <expand macro="output_illumina_microsat_summary" />
178 <output name="output_pal_summary" file="illuminaPE_microsats.out" /> 183 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
179 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats.out" /> 184 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats.out.re_match" />
180 <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" /> 185 <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" />
181 </test> 186 </test>
182 <test> 187 <!-- Test with Illumina input as dataset pair -->
183 <!-- Test with Illumina input as dataset pair --> 188 <test>
184 <param name="platform_type" value="illumina" /> 189 <param name="platform_type" value="illumina" />
185 <param name="paired_input_type" value="collection" /> 190 <param name="paired_input_type" value="collection" />
186 <param name="input_fastq_pair"> 191 <param name="input_fastq_pair">
187 <collection type="paired"> 192 <collection type="paired">
188 <element name="forward" value="illuminaPE_r1.fq" ftype="fastqsanger" /> 193 <element name="forward" value="illuminaPE_r1.fq" ftype="fastqsanger" />
189 <element name="reverse" value="illuminaPE_r2.fq" ftype="fastqsanger" /> 194 <element name="reverse" value="illuminaPE_r2.fq" ftype="fastqsanger" />
190 </collection> 195 </collection>
191 </param> 196 </param>
192 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> 197 <expand macro="output_illumina_microsat_summary" />
193 <output name="output_pal_summary" file="illuminaPE_microsats.out" /> 198 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
194 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats.out" /> 199 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats.out.re_match" />
195 <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" /> 200 <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" />
196 </test> 201 </test>
197 <test> 202 <!-- Test with Illumina input filter to loci with PandaSEQ assembly
198 <!-- Test with Illumina input filter to loci with PandaSEQ assembly 203 ('-assembly' option)
199 ('-assembly' option) --> 204 -->
205 <test>
200 <param name="platform_type" value="illumina" /> 206 <param name="platform_type" value="illumina" />
201 <param name="filters" value="" /> 207 <param name="filters" value="" />
202 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> 208 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
203 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> 209 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
204 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> 210 <expand macro="output_illumina_microsat_summary" />
205 <output name="output_pal_summary" file="illuminaPE_microsats.out" /> 211 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
206 <output name="output_assembly" file="illuminaPE_assembly.out" /> 212 <output name="output_assembly" file="illuminaPE_assembly.out" />
207 </test> 213 </test>
208 <test> 214 <!-- Test with Illumina input filter to loci with primers
209 <!-- Test with Illumina input filter to loci with primers 215 ('-primers' option) -->
210 ('-primers' option) --> 216 <test>
211 <param name="platform_type" value="illumina" /> 217 <param name="platform_type" value="illumina" />
212 <param name="filters" value="-primers" /> 218 <param name="filters" value="-primers" />
213 <param name="assembly" value="false" /> 219 <param name="assembly" value="false" />
214 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> 220 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
215 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> 221 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
216 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> 222 <expand macro="output_illumina_microsat_summary" />
217 <output name="output_pal_summary" file="illuminaPE_microsats.out" /> 223 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
218 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_primers.out" /> 224 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_primers.out.re_match" />
219 </test> 225 </test>
220 <test> 226 <!-- Test with Illumina input filter to loci which appear only once
221 <!-- Test with Illumina input filter to loci which appear only once 227 ('-occurrences' option) -->
222 ('-occurrences' option) --> 228 <test>
223 <param name="platform_type" value="illumina" /> 229 <param name="platform_type" value="illumina" />
224 <param name="filters" value="-occurrences" /> 230 <param name="filters" value="-occurrences" />
225 <param name="assembly" value="false" /> 231 <param name="assembly" value="false" />
226 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> 232 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
227 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> 233 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
228 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> 234 <expand macro="output_illumina_microsat_summary" />
229 <output name="output_pal_summary" file="illuminaPE_microsats.out" /> 235 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
230 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_occurrences.out" /> 236 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_occurrences.out.re_match" />
231 </test> 237 </test>
232 <test> 238 <!-- Test with Illumina input filter and rank loci with perfect motifs
233 <!-- Test with Illumina input filter and rank loci with perfect motifs 239 ('-rankmotifs' option) -->
234 ('-rankmotifs' option) --> 240 <test>
235 <param name="platform_type" value="illumina" /> 241 <param name="platform_type" value="illumina" />
236 <param name="filters" value="-rankmotifs" /> 242 <param name="filters" value="-rankmotifs" />
237 <param name="assembly" value="false" /> 243 <param name="assembly" value="false" />
238 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> 244 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
239 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> 245 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
240 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> 246 <expand macro="output_illumina_microsat_summary" />
241 <output name="output_pal_summary" file="illuminaPE_microsats.out" /> 247 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
242 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats_rankmotifs.out" /> 248 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_rankmotifs.out.re_match" />
243 </test> 249 </test>
244 <test> 250 <!-- Test with 454 input -->
245 <!-- Test with 454 input --> 251 <test>
246 <param name="platform_type" value="454" /> 252 <param name="platform_type" value="454" />
247 <param name="input_fasta" value="454_in.fa" ftype="fasta" /> 253 <param name="input_fasta" value="454_in.fa" ftype="fasta" />
248 <output name="output_microsat_summary" file="454_microsat_types.out" /> 254 <expand macro="output_454_microsat_summary" />
249 <output name="output_pal_summary" file="454_microsats.out" /> 255 <output name="output_pal_summary" compare="re_match" file="454_microsats.out.re_match" />
250 </test> 256 </test>
251 </tests> 257 </tests>
252 <help> 258 <help>
253 .. class:: infomark 259 .. class:: infomark
254 260
269 present in high-quality assembly 275 present in high-quality assembly
270 276
271 Pal_finder runs the primer3_core program; information on the settings used in 277 Pal_finder runs the primer3_core program; information on the settings used in
272 primer3_core can be found in the Primer3 manual at 278 primer3_core can be found in the Primer3 manual at
273 http://primer3.sourceforge.net/primer3_manual.htm 279 http://primer3.sourceforge.net/primer3_manual.htm
274
275 -------------
276
277 .. class:: warning
278
279 **Known problems**
280
281 .. class:: infomark
282
283 **Bad primer product size ranges**
284
285 For some datasets pal_finder may generate 'bad' product size ranges (where the
286 lower limit exceeds the upper limit) for one or more reads, for input into
287 primer3_core.
288
289 If this occurs then the tool will terminate with an error. A list of the reads
290 for which the bad ranges were generated can be found in the error message
291 which can be accessed via the 'bug' icon from a failed dataset.
292
293 The conditions which cause this error are unclear. However we believe it to be
294 associated with short or low quality reads. It is recommended that the input
295 data are sufficiently trimmed and filtered (using e.g. the Trimmomatic tool)
296 before rerunning pal_finder.
297 280
298 ------------- 281 -------------
299 282
300 .. class:: infomark 283 .. class:: infomark
301 284