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comparison pal_finder_wrapper.xml @ 14:3f8bf1a0403b draft

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Uploaded version with bad primer ranger detection (WIP).
author pjbriggs
date Thu, 22 Mar 2018 07:21:26 -0400
parents d26fb5260c67
children a3af1ff4cad1
comparison
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13:88c972081f15 14:3f8bf1a0403b
1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.6"> 1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.7">
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> 3 <macros>
4 <import>pal_finder_macros.xml</import> 4 <import>pal_finder_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
24 #end if 24 #end if
25 #else 25 #else
26 --454 "$platform.input_fasta" 26 --454 "$platform.input_fasta"
27 #end if 27 #end if
28 $output_microsat_summary $output_pal_summary 28 $output_microsat_summary $output_pal_summary
29 #if $report_bad_primer_ranges
30 --bad_primer_ranges "$output_bad_primer_read_ids"
31 #end if
29 #if $keep_config_file 32 #if $keep_config_file
30 --output_config_file "$output_config_file" 33 --output_config_file "$output_config_file"
31 #end if 34 #end if
32 --primer-prefix "$primer_prefix" 35 --primer-prefix "$primer_prefix"
33 --2merMinReps $min_2mer_repeats 36 --2merMinReps $min_2mer_repeats
154 <param name="primer_pair_max_diff_tm" type="float" value="2.0" 157 <param name="primer_pair_max_diff_tm" type="float" value="2.0"
155 label="Maximum acceptable difference between melting temperatures of left and right primers (PRIMER_PAIR_MAX_DIFF_TM)" 158 label="Maximum acceptable difference between melting temperatures of left and right primers (PRIMER_PAIR_MAX_DIFF_TM)"
156 help="Temperature should be in degrees Celsius" /> 159 help="Temperature should be in degrees Celsius" />
157 </when> 160 </when>
158 </conditional> 161 </conditional>
162 <param name="report_bad_primer_ranges" type="boolean" truevalue="True" falsevalue="False" label="Output IDs for input reads which generate bad primer ranges" help="Can be used to screen input Fastqs" />
159 <param name="keep_config_file" type="boolean" truevalue="True" falsevalue="False" 163 <param name="keep_config_file" type="boolean" truevalue="True" falsevalue="False"
160 label="Output the config file to the history" 164 label="Output the config file to the history"
161 help="Can be used to run pal_finder outside of Galaxy" /> 165 help="Can be used to run pal_finder outside of Galaxy" />
162 </inputs> 166 </inputs>
163 <outputs> 167 <outputs>
167 </data> 171 </data>
168 <data name="output_microsat_summary" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: summary of microsatellite types" /> 172 <data name="output_microsat_summary" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: summary of microsatellite types" />
169 <data name="output_assembly" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: assembly"> 173 <data name="output_assembly" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: assembly">
170 <filter>platform['assembly'] is True</filter> 174 <filter>platform['assembly'] is True</filter>
171 </data> 175 </data>
176 <data name="output_bad_primer_read_ids" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: read IDs generating bad primer ranges">
177 <filter>report_bad_primer_ranges is True</filter>
178 </data>
172 <data name="output_config_file" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: config file"> 179 <data name="output_config_file" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: config file">
173 <filter>keep_config_file is True</filter> 180 <filter>keep_config_file is True</filter>
174 </data> 181 </data>
175 </outputs> 182 </outputs>
176 <tests> 183 <tests>
245 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> 252 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
246 <expand macro="output_illumina_microsat_summary" /> 253 <expand macro="output_illumina_microsat_summary" />
247 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" /> 254 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
248 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_rankmotifs.out.re_match" /> 255 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_rankmotifs.out.re_match" />
249 </test> 256 </test>
257 <!-- Test with Illumina input generating bad primer ranges
258 -->
259 <test>
260 <param name="platform_type" value="illumina" />
261 <param name="filters" value="" />
262 <param name="assembly" value="false" />
263 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
264 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
265 <param name="output_bad_primer_read_ids" value="true" />
266 <expand macro="output_illumina_microsat_summary" />
267 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
268 <output name="output_bad_primer_read_ids" file="illuminaPE_bad_primer_ids.out" />
269 </test>
250 <!-- Test with 454 input --> 270 <!-- Test with 454 input -->
251 <test> 271 <test>
252 <param name="platform_type" value="454" /> 272 <param name="platform_type" value="454" />
253 <param name="input_fasta" value="454_in.fa" ftype="fasta" /> 273 <param name="input_fasta" value="454_in.fa" ftype="fasta" />
254 <expand macro="output_454_microsat_summary" /> 274 <expand macro="output_454_microsat_summary" />
275 present in high-quality assembly 295 present in high-quality assembly
276 296
277 Pal_finder runs the primer3_core program; information on the settings used in 297 Pal_finder runs the primer3_core program; information on the settings used in
278 primer3_core can be found in the Primer3 manual at 298 primer3_core can be found in the Primer3 manual at
279 http://primer3.sourceforge.net/primer3_manual.htm 299 http://primer3.sourceforge.net/primer3_manual.htm
300
301 -------------
302
303 .. class:: warning
304
305 **Known problems**
306
307 .. class:: infomark
308
309 **Bad primer product size ranges**
310
311 For some datasets pal_finder may generate 'bad' product size ranges (where the
312 lower limit exceeds the upper limit) for one or more reads, for input into
313 primer3_core.
314
315 If this occurs then the tool will terminate with an error. A list of the reads
316 for which the bad ranges were generated can be found in the error message
317 which can be accessed via the 'bug' icon from a failed dataset.
318
319 The conditions which cause this error are unclear. However we believe it to be
320 associated with short or low quality reads. It is recommended that the input
321 data are sufficiently trimmed and filtered (using e.g. the Trimmomatic tool)
322 before rerunning pal_finder.
280 323
281 ------------- 324 -------------
282 325
283 .. class:: infomark 326 .. class:: infomark
284 327