Mercurial > repos > pjbriggs > pal_finder

comparison pal_finder_wrapper.xml @ 7:5e133b7b79a6 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded version 0.02.04.6 (uses conda dependency resolution).
author pjbriggs
date Mon, 19 Mar 2018 06:33:32 -0400
parents a73c48890bde
children 4e625d3672ba
comparison
equal deleted inserted replaced
6:a73c48890bde 7:5e133b7b79a6
1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.5"> 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