Mercurial > repos > pjbriggs > pal_finder
comparison pal_finder_wrapper.xml @ 7:5e133b7b79a6 draft
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 |
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| 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 |