Mercurial > repos > pjbriggs > pal_finder
annotate pal_finder_wrapper.xml @ 1:771ebe02636f draft
Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
| author | pjbriggs |
|---|---|
| date | Mon, 23 Mar 2015 07:01:37 -0400 |
| parents | 3f908e7fff4f |
| children | b6ccc7dd7b02 |
| rev | line source |
|---|---|
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1
771ebe02636f
Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
pjbriggs
parents:
0
diff
changeset
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1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.2"> |
| 0 | 2 <description>Find microsatellite repeat elements sequencing reads and design PCR primers to amplify them</description> |
| 3 <command interpreter="bash">pal_finder_wrapper.sh | |
| 4 #if str( $platform.platform_type ) == "illumina" | |
| 5 $platform.input_fastq_r1 $platform.input_fastq_r2 | |
| 6 #else | |
| 7 --454 $platform.input_fasta | |
| 8 #end if | |
| 9 $output_microsat_summary $output_pal_summary | |
| 10 #if str( $platform.platform_type ) == "illumina" and $platform.filter_microsats | |
| 11 --filter_microsats $output_filtered_microsats | |
| 12 #end if | |
| 13 #if $keep_config_file | |
| 14 --output_config_file $output_config_file | |
| 15 #end if | |
|
1
771ebe02636f
Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
pjbriggs
parents:
0
diff
changeset
|
16 --primer-prefix "$primer_prefix" |
| 0 | 17 --2merMinReps $min_2mer_repeats |
| 18 --3merMinReps $min_3mer_repeats | |
| 19 --4merMinReps $min_4mer_repeats | |
| 20 --5merMinReps $min_5mer_repeats | |
| 21 --6merMinReps $min_6mer_repeats | |
| 22 #if str( $primer.primer_options ) == "custom" | |
| 23 --primer-opt-size $primer.primer_opt_size | |
| 24 --primer-min-size $primer.primer_min_size | |
| 25 --primer-max-size $primer.primer_max_size | |
| 26 --primer-min-gc $primer.primer_min_gc | |
| 27 --primer-max-gc $primer.primer_max_gc | |
| 28 --primer-gc-clamp $primer.primer_gc_clamp | |
| 29 --primer-max-end-gc $primer.primer_max_end_gc | |
| 30 --primer-min-tm $primer.primer_min_tm | |
| 31 --primer-max-tm $primer.primer_max_tm | |
| 32 --primer-opt-tm $primer.primer_opt_tm | |
| 33 --primer-pair-max-diff-tm $primer.primer_pair_max_diff_tm | |
| 34 #end if | |
| 35 #if str( $mispriming.mispriming_options ) == "custom" | |
| 36 --primer-mispriming-library $mispriming.mispriming_library | |
| 37 #end if | |
| 38 </command> | |
| 39 <requirements> | |
|
1
771ebe02636f
Uploaded version 0.02.04.2: fix bug that causes tool to fail when prefix includes spaces; add explicit dependency on Perl 5.16.3.
pjbriggs
parents:
0
diff
changeset
|
40 <requirement type="package" version="5.16.3">perl</requirement> |
| 0 | 41 <requirement type="package" version="0.02.04">pal_finder</requirement> |
| 42 <requirement type="package" version="2.0.0">primer3_core</requirement> | |
| 43 </requirements> | |
| 44 <inputs> | |
| 45 <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" /> | |
| 46 <conditional name="platform"> | |
| 47 <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" > | |
| 48 <option value="illumina" selected="true">Illumina</option> | |
| 49 <option value="454">454</option> | |
| 50 </param> | |
| 51 <when value="illumina"> | |
| 52 <param name="input_fastq_r1" type="data" format="fastqsanger" label="Illumina fastq file (read 1)" /> | |
| 53 <param name="input_fastq_r2" type="data" format="fastqsanger" label="Illumina fastq file (read 2)" /> | |
| 54 <param name="filter_microsats" type="boolean" truevalue="True" falsevalue="False" | |
| 55 label="Filter and sort the microsatellites" checked="True" | |
| 56 help="Filter pal_finder results to only include lines with primer sequences and remove non-perfect repeats" /> | |
| 57 </when> | |
| 58 <when value="454"> | |
| 59 <param name="input_fasta" type="data" format="fasta" label="454 fasta file with raw reads" /> | |
| 60 </when> | |
| 61 </conditional> | |
| 62 <param name="min_2mer_repeats" type="integer" value="6" label="Minimum number of 2-mer repeat units to detect" help="Set to zero to ignore repeats of this n-mer unit" /> | |
| 63 <param name="min_3mer_repeats" type="integer" value="0" label="Minimum number of 3-mer repeat units" help="Set to zero to ignore repeats of this n-mer unit" /> | |
| 64 <param name="min_4mer_repeats" type="integer" value="0" label="Minimum number of 4-mer repeat units" help="Set to zero to ignore repeats of this n-mer unit" /> | |
| 65 <param name="min_5mer_repeats" type="integer" value="0" label="Minimum number of 5-mer repeat units" help="Set to zero to ignore repeats of this n-mer unit" /> | |
| 66 <param name="min_6mer_repeats" type="integer" value="0" label="Minimum number of 6-mer repeat units" help="Set to zero to ignore repeats of this n-mer unit" /> | |
| 67 <conditional name="mispriming"> | |
| 68 <param name="mispriming_options" type="select" label="Mispriming library to use" help="Specify file of nucleotide sequences to avoid amplifying (PRIMER_MISPRIMING_LIBRARY)"> | |
| 69 <option value="default">Default from pal_finder</option> | |
| 70 <option value="custom">Custom sequences from history</option> | |
| 71 </param> | |
| 72 <when value="default"> | |
| 73 </when> | |
| 74 <when value="custom"> | |
| 75 <param name="mispriming_library" type="data" format="fasta" label="Select mispriming library from history" help="Fasta file containing sequences to avoid amplifying" /> | |
| 76 </when> | |
| 77 </conditional> | |
| 78 <conditional name="primer"> | |
| 79 <param name="primer_options" type="select" label="Primer settings to use" help="Advanced users can customise the settings for primer3 for more control"> | |
| 80 <option value="default">Defaults for pal_finder</option> | |
| 81 <option value="custom">Custom</option> | |
| 82 </param> | |
| 83 <when value="custom"> | |
| 84 <param name="primer_opt_size" type="integer" value="20" | |
| 85 label="Optimum length (in bases) of a primer (PRIMER_OPT_SIZE)" | |
| 86 help="Primer3 will attempt to pick primers close to this length" /> | |
| 87 <param name="primer_min_size" type="integer" value="18" | |
| 88 label="Minimum acceptable length (in bases) of a primer (PRIMER_MIN_SIZE)" | |
| 89 help="Must be greater than 0 and less than or equal to PRIMER_MAX_SIZE" /> | |
| 90 <param name="primer_max_size" type="integer" value="30" | |
| 91 label="Maximum acceptable length (in bases) of a primer (PRIMER_MAX_SIZE)" | |
| 92 help="Currently this parameter cannot be larger than 35. This limit is governed by maximum oligo size for which primer3's melting-temperature is valid" /> | |
| 93 <param name="primer_min_gc" type="float" value="30.0" | |
| 94 label="Minimum allowable percentage of Gs and Cs in any primer (PRIMER_MIN_GC)" /> | |
| 95 <param name="primer_max_gc" type="float" value="80.0" | |
| 96 label="Maximum allowable percentage of Gs and Cs in any primer (PRIMER_MAX_GC)" /> | |
| 97 <param name="primer_gc_clamp" type="integer" value="2" | |
| 98 label="Specify number of consecutive Gs and Cs at 3' end of both the left and right primer (PRIMER_GC_CLAMP)" /> | |
| 99 <param name="primer_max_end_gc" type="integer" value="5" | |
| 100 label="Maximum number of Gs or Cs allowed in last five 3' bases of a left or right primer (PRIMER_MAX_END_GC)" /> | |
| 101 <param name="primer_min_tm" type="float" value="58.0" | |
| 102 label="Minimum acceptable melting temperature for a primer oligo (PRIMER_MIN_TM)" | |
| 103 help="Temperature should be in degrees Celsius" /> | |
| 104 <param name="primer_max_tm" type="float" value="65.0" | |
| 105 label="Maximum acceptable melting temperature for a primer oligo (PRIMER_MAX_TM)" | |
| 106 help="Temperature should be in degrees Celsius" /> | |
| 107 <param name="primer_opt_tm" type="float" value="62.0" | |
| 108 label="Optimum melting temperature for a primer (PRIMER_OPT_TM)" | |
| 109 help="Temperature should be in degrees Celsius" /> | |
| 110 <param name="primer_pair_max_diff_tm" type="float" value="2.0" | |
| 111 label="Maximum acceptable difference between melting temperatures of left and right primers (PRIMER_PAIR_MAX_DIFF_TM)" | |
| 112 help="Temperature should be in degrees Celsius" /> | |
| 113 </when> | |
| 114 </conditional> | |
| 115 <param name="keep_config_file" type="boolean" truevalue="True" falsevalue="False" | |
| 116 label="Output the config file to the history" | |
| 117 help="Can be used to run pal_finder outside of Galaxy" /> | |
| 118 </inputs> | |
| 119 <outputs> | |
| 120 <data name="output_microsat_summary" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix} (microsatellite types)" /> | |
| 121 <data name="output_pal_summary" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix} (microsatellites with read IDs and primer pairs)" /> | |
| 122 <data name="output_filtered_microsats" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix} (filtered and sorted microsatellites)"> | |
| 123 <filter>platform['platform_type'] == 'illumina' and platform['filter_microsats']</filter> | |
| 124 </data> | |
| 125 <data name="output_config_file" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix} (config file)"> | |
| 126 <filter>keep_config_file is True</filter> | |
| 127 </data> | |
| 128 </outputs> | |
| 129 <tests> | |
| 130 <test> | |
| 131 <!-- Test with Illumina input --> | |
| 132 <param name="platform_type" value="illumina" /> | |
| 133 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" /> | |
| 134 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" /> | |
| 135 <!-- | |
| 136 **NB** outputs have to be specified in order that they appear in the | |
| 137 tool (which is the order they will be written to the history) - the | |
| 138 test framework seems to use the order and ignores the "name" attribute | |
| 139 --> | |
| 140 <output name="output_microsat_summary" file="illuminaPE_microsat_types.out" /> | |
| 141 <output name="output_pal_summary" file="illuminaPE_microsats.out" /> | |
| 142 <output name="output_filtered_microsats" file="illuminaPE_filtered_microsats.out" /> | |
| 143 </test> | |
| 144 <test> | |
| 145 <!-- Test with 454 input --> | |
| 146 <param name="platform_type" value="454" /> | |
| 147 <param name="input_fasta" value="454_in.fa" ftype="fasta" /> | |
| 148 <!-- | |
| 149 **NB** outputs have to be specified in order that they appear in the | |
| 150 tool (which is the order they will be written to the history) - the | |
| 151 test framework seems to use the order and ignores the "name" attribute | |
| 152 --> | |
| 153 <output name="output_microsat_summary" file="454_microsat_types.out" /> | |
| 154 <output name="output_pal_summary" file="454_microsats.out" /> | |
| 155 </test> | |
| 156 </tests> | |
| 157 <help> | |
| 158 .. class:: infomark | |
| 159 | |
| 160 **What it does** | |
| 161 | |
| 162 This tool runs the pal_finder program, which finds microsatellite repeat elements | |
| 163 directly from raw 454 or Illumina paired-end sequencing reads. It then designs PCR | |
| 164 primers to amplify these repeat loci (Potentially Amplifiable Loci: PAL). | |
| 165 | |
| 166 Optionally for Illumina data, the output from pal_finder can also be filtered to | |
| 167 remove any motifs without primer sequences, and with non-perfect microsatellites. | |
| 168 The microsatellites are then ranked by motif size (largest to smallest). | |
| 169 | |
| 170 Pal_finder runs the primer3_core program; information on the settings used in | |
| 171 primer3_core can be found in the Primer3 manual at | |
| 172 http://primer3.sourceforge.net/primer3_manual.htm | |
| 173 | |
| 174 ------------- | |
| 175 | |
| 176 .. class:: infomark | |
| 177 | |
| 178 **Credits** | |
| 179 | |
| 180 This Galaxy tool has been developed by Peter Briggs within the Bioinformatics Core | |
| 181 Facility at the University of Manchester. It runs the pal_finder package which can be | |
| 182 obtained from http://sourceforge.net/projects/palfinder/: | |
| 183 | |
| 184 * PLoS One. 2012; 7(2): e30953 "Rapid Microsatellite Identification from Illumina Paired-End | |
| 185 Genomic Sequencing in Two Birds and a Snake" Todd A. Castoe, Alexander W. Poole, A. P. | |
| 186 Jason de Koning, Kenneth L. Jones, Diana F. Tomback, Sara J. Oyler-McCance, Jennifer A. | |
| 187 Fike, Stacey L. Lance, Jeffrey W. Streicher, Eric N. Smith, and David D. Pollock | |
| 188 | |
| 189 The paper is available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279355/ | |
| 190 | |
| 191 This tool is compatible with pal_finder version 0.02.04, which in turn runs the | |
| 192 primer3_core program (version 2.0.0-alpha is required, available from | |
| 193 http://primer3.sourceforge.net/releases.php): | |
| 194 | |
| 195 * Steve Rozen and Helen J. Skaletsky (2000) "Primer3 on the WWW for general users and for | |
| 196 biologist programmers". In: Krawetz S, Misener S (eds) Bioinformatics Methods and | |
| 197 Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386 | |
| 198 | |
| 199 The paper is available at | |
| 200 http://purl.com/STEVEROZEN/papers/rozen-and-skaletsky-2000-primer3.pdf | |
| 201 | |
| 202 The filtering and sorting of the pal_finder output for Illumina data is performed | |
| 203 using a Perl script written by Graeme Fox at the University of Manchester, and which | |
| 204 is included with this tool. | |
| 205 | |
| 206 Please kindly acknowledge both this Galaxy tool, the pal_finder and primer3 packages, and | |
| 207 the utility script if you use it in your work. | |
| 208 </help> | |
| 209 <citations> | |
| 210 <!-- | |
| 211 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set | |
| 212 Can be either DOI or Bibtex | |
| 213 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex | |
| 214 --> | |
| 215 <citation type="doi">10.1371/journal.pone.0030953</citation> | |
| 216 <citation type="bibtex">@Article{pmid10547847, | |
| 217 Author="Rozen, S. and Skaletsky, H. ", | |
| 218 Title="{{P}rimer3 on the {W}{W}{W} for general users and for biologist programmers}", | |
| 219 Journal="Methods Mol. Biol.", | |
| 220 Year="2000", | |
| 221 Volume="132", | |
| 222 Pages="365--386", | |
| 223 URL="{http://purl.com/STEVEROZEN/papers/rozen-and-skaletsky-2000-primer3.pdf}" | |
| 224 }</citation> | |
| 225 </citations> | |
| 226 </tool> |