annotate 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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
1 <tool id="microsat_pal_finder" name="pal_finder" version="0.02.04.6">
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
2 <description>Find microsatellite repeat elements from sequencing reads and design PCR primers to amplify them</description>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
3 <macros>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
4 <import>pal_finder_macros.xml</import>
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
5 </macros>
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
6 <requirements>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
7 <requirement type="package" version="0.02.04">pal_finder</requirement>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
8 <requirement type="package" version="2.7">python</requirement>
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
9 <requirement type="package" version="1.65">biopython</requirement>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
10 <requirement type="package" version="2.8.1">pandaseq</requirement>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
11 </requirements>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
12 <command><![CDATA[
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
13 @CONDA_PAL_FINDER_SCRIPT_DIR@ &&
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
14 @CONDA_PAL_FINDER_DATA_DIR@ &&
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
15 bash $__tool_directory__/pal_finder_wrapper.sh
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
16 #if str( $platform.platform_type ) == "illumina"
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
17 #set $paired_input_type = $platform.paired_input_type_conditional.paired_input_type
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
18 #if $paired_input_type == "pair_of_files"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
19 "$platform.paired_input_type_conditional.input_fastq_r1"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
20 "$platform.paired_input_type_conditional.input_fastq_r2"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
21 #else
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
22 "$platform.paired_input_type_conditional.input_fastq_pair.forward"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
23 "$platform.paired_input_type_conditional.input_fastq_pair.reverse"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
24 #end if
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
25 #else
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
26 --454 "$platform.input_fasta"
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
27 #end if
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
28 $output_microsat_summary $output_pal_summary
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
29 #if $keep_config_file
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
30 --output_config_file "$output_config_file"
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
31 #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
32 --primer-prefix "$primer_prefix"
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
33 --2merMinReps $min_2mer_repeats
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
34 --3merMinReps $min_3mer_repeats
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
35 --4merMinReps $min_4mer_repeats
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
36 --5merMinReps $min_5mer_repeats
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
37 --6merMinReps $min_6mer_repeats
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
38 #if str( $primer.primer_options ) == "custom"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
39 --primer-opt-size $primer.primer_opt_size
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
40 --primer-min-size $primer.primer_min_size
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
41 --primer-max-size $primer.primer_max_size
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
42 --primer-min-gc $primer.primer_min_gc
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
43 --primer-max-gc $primer.primer_max_gc
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
44 --primer-gc-clamp $primer.primer_gc_clamp
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
45 --primer-max-end-gc $primer.primer_max_end_gc
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
46 --primer-min-tm $primer.primer_min_tm
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
47 --primer-max-tm $primer.primer_max_tm
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
48 --primer-opt-tm $primer.primer_opt_tm
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
49 --primer-pair-max-diff-tm $primer.primer_pair_max_diff_tm
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
50 #end if
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
51 #if str( $mispriming.mispriming_options ) == "custom"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
52 --primer-mispriming-library $mispriming.mispriming_library
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
53 #end if
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
54 #if str( $platform.platform_type ) == "illumina"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
55 #if $platform.filters
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
56 #for $filter in str($platform.filters).split(',')
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
57 $filter
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
58 --filter_microsats "$output_filtered_microsats"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
59 #end for
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
60 #end if
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
61 #if str( $platform.assembly ) == '-assembly'
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
62 $platform.assembly "$output_assembly"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
63 #end if
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
64 #end if
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
65 ]]></command>
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
66 <inputs>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
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" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
68 <conditional name="platform">
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
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" >
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
70 <option value="illumina" selected="true">Illumina</option>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
71 <option value="454">454</option>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
72 </param>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
73 <when value="illumina">
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
74 <conditional name="paired_input_type_conditional">
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
75 <param name="paired_input_type" type="select" label="Input Type">
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
76 <option value="pair_of_files" selected="true">Pair of datasets</option>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
77 <option value="collection">Dataset collection pair</option>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
78 </param>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
79 <when value="pair_of_files">
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
80 <param name="input_fastq_r1" type="data" format="fastqsanger"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
81 label="Illumina fastq file (read 1)" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
82 <param name="input_fastq_r2" type="data" format="fastqsanger"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
83 label="Illumina fastq file (read 2)" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
84 </when>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
85 <when value="collection">
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
86 <param name="input_fastq_pair" format="fastqsanger"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
87 type="data_collection" collection_type="paired"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
88 label="Select FASTQ dataset collection with R1/R2 pair" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
89 </when>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
90 </conditional>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
91 <param name="filters" type="select" display="checkboxes"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
92 multiple="True" label="Filters to apply to the pal_finder results"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
93 help="Apply none, one or more filters to refine results">
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
94 <option value="-primers" selected="True">Only include loci with designed primers</option>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
95 <option value="-occurrences" selected="True">Exclude loci where the primer sequences occur more than once in the reads</option>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
96 <option value="-rankmotifs" selected="True">Only include loci with 'perfect' motifs, and rank by motif size</option>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
97 </param>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
98 <param name="assembly" type="boolean"
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
99 checked="True" truevalue="-assembly" falsevalue=""
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
100 label="Use PANDAseq to assemble paired-end reads and confirm primer sequences are present in high-quality assembly" />
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
101 </when>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
102 <when value="454">
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
103 <param name="input_fasta" type="data" format="fasta" label="454 fasta file with raw reads" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
104 </when>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
105 </conditional>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
106 <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" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
107 <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" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
108 <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" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
109 <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" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
110 <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" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
111 <conditional name="mispriming">
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
112 <param name="mispriming_options" type="select" label="Mispriming library to use" help="Specify file of nucleotide sequences to avoid amplifying (PRIMER_MISPRIMING_LIBRARY)">
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
113 <option value="default">Default from pal_finder</option>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
114 <option value="custom">Custom sequences from history</option>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
115 </param>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
116 <when value="default">
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
117 </when>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
118 <when value="custom">
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
119 <param name="mispriming_library" type="data" format="fasta" label="Select mispriming library from history" help="Fasta file containing sequences to avoid amplifying" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
120 </when>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
121 </conditional>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
122 <conditional name="primer">
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
123 <param name="primer_options" type="select" label="Primer settings to use" help="Advanced users can customise the settings for primer3 for more control">
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
124 <option value="default">Defaults for pal_finder</option>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
125 <option value="custom">Custom</option>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
126 </param>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
127 <when value="custom">
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
128 <param name="primer_opt_size" type="integer" value="20"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
129 label="Optimum length (in bases) of a primer (PRIMER_OPT_SIZE)"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
130 help="Primer3 will attempt to pick primers close to this length" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
131 <param name="primer_min_size" type="integer" value="18"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
132 label="Minimum acceptable length (in bases) of a primer (PRIMER_MIN_SIZE)"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
133 help="Must be greater than 0 and less than or equal to PRIMER_MAX_SIZE" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
134 <param name="primer_max_size" type="integer" value="30"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
135 label="Maximum acceptable length (in bases) of a primer (PRIMER_MAX_SIZE)"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
136 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" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
137 <param name="primer_min_gc" type="float" value="30.0"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
138 label="Minimum allowable percentage of Gs and Cs in any primer (PRIMER_MIN_GC)" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
139 <param name="primer_max_gc" type="float" value="80.0"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
140 label="Maximum allowable percentage of Gs and Cs in any primer (PRIMER_MAX_GC)" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
141 <param name="primer_gc_clamp" type="integer" value="2"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
142 label="Specify number of consecutive Gs and Cs at 3' end of both the left and right primer (PRIMER_GC_CLAMP)" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
143 <param name="primer_max_end_gc" type="integer" value="5"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
144 label="Maximum number of Gs or Cs allowed in last five 3' bases of a left or right primer (PRIMER_MAX_END_GC)" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
145 <param name="primer_min_tm" type="float" value="58.0"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
146 label="Minimum acceptable melting temperature for a primer oligo (PRIMER_MIN_TM)"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
147 help="Temperature should be in degrees Celsius" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
148 <param name="primer_max_tm" type="float" value="65.0"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
149 label="Maximum acceptable melting temperature for a primer oligo (PRIMER_MAX_TM)"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
150 help="Temperature should be in degrees Celsius" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
151 <param name="primer_opt_tm" type="float" value="62.0"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
152 label="Optimum melting temperature for a primer (PRIMER_OPT_TM)"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
153 help="Temperature should be in degrees Celsius" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
154 <param name="primer_pair_max_diff_tm" type="float" value="2.0"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
155 label="Maximum acceptable difference between melting temperatures of left and right primers (PRIMER_PAIR_MAX_DIFF_TM)"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
156 help="Temperature should be in degrees Celsius" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
157 </when>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
158 </conditional>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
159 <param name="keep_config_file" type="boolean" truevalue="True" falsevalue="False"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
160 label="Output the config file to the history"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
161 help="Can be used to run pal_finder outside of Galaxy" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
162 </inputs>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
163 <outputs>
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
164 <data name="output_pal_summary" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: all microsatellites (full details)" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
165 <data name="output_filtered_microsats" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: filtered microsatellites (full details)">
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
166 <filter>platform['platform_type'] == 'illumina' and platform['filters'] is not None</filter>
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
167 </data>
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
168 <data name="output_microsat_summary" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: summary of microsatellite types" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
169 <data name="output_assembly" format="tabular" label="${tool.name} on ${on_string} for ${primer_prefix}: assembly">
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
170 <filter>platform['assembly'] is True</filter>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
171 </data>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
172 <data name="output_config_file" format="txt" label="${tool.name} on ${on_string} for ${primer_prefix}: config file">
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
173 <filter>keep_config_file is True</filter>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
174 </data>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
175 </outputs>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
176 <tests>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
177 <!-- Test with Illumina input -->
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
178 <test>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
179 <param name="platform_type" value="illumina" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
180 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
181 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
182 <expand macro="output_illumina_microsat_summary" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
183 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
184 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats.out.re_match" />
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
185 <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
186 </test>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
187 <!-- Test with Illumina input as dataset pair -->
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
188 <test>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
189 <param name="platform_type" value="illumina" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
190 <param name="paired_input_type" value="collection" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
191 <param name="input_fastq_pair">
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
192 <collection type="paired">
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
193 <element name="forward" value="illuminaPE_r1.fq" ftype="fastqsanger" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
194 <element name="reverse" value="illuminaPE_r2.fq" ftype="fastqsanger" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
195 </collection>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
196 </param>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
197 <expand macro="output_illumina_microsat_summary" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
198 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
199 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats.out.re_match" />
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
200 <output name="output_assembly" file="illuminaPE_assembly_after_filters.out" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
201 </test>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
202 <!-- Test with Illumina input filter to loci with PandaSEQ assembly
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
203 ('-assembly' option)
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
204 -->
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
205 <test>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
206 <param name="platform_type" value="illumina" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
207 <param name="filters" value="" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
208 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
209 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
210 <expand macro="output_illumina_microsat_summary" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
211 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
212 <output name="output_assembly" file="illuminaPE_assembly.out" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
213 </test>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
214 <!-- Test with Illumina input filter to loci with primers
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
215 ('-primers' option) -->
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
216 <test>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
217 <param name="platform_type" value="illumina" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
218 <param name="filters" value="-primers" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
219 <param name="assembly" value="false" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
220 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
221 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
222 <expand macro="output_illumina_microsat_summary" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
223 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
224 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_primers.out.re_match" />
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
225 </test>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
226 <!-- Test with Illumina input filter to loci which appear only once
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
227 ('-occurrences' option) -->
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
228 <test>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
229 <param name="platform_type" value="illumina" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
230 <param name="filters" value="-occurrences" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
231 <param name="assembly" value="false" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
232 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
233 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
234 <expand macro="output_illumina_microsat_summary" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
235 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
236 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_occurrences.out.re_match" />
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
237 </test>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
238 <!-- Test with Illumina input filter and rank loci with perfect motifs
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
239 ('-rankmotifs' option) -->
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
240 <test>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
241 <param name="platform_type" value="illumina" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
242 <param name="filters" value="-rankmotifs" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
243 <param name="assembly" value="false" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
244 <param name="input_fastq_r1" value="illuminaPE_r1.fq" ftype="fastqsanger" />
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
245 <param name="input_fastq_r2" value="illuminaPE_r2.fq" ftype="fastqsanger" />
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
246 <expand macro="output_illumina_microsat_summary" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
247 <output name="output_pal_summary" compare="re_match" file="illuminaPE_microsats.out.re_match" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
248 <output name="output_filtered_microsats" compare="re_match" file="illuminaPE_filtered_microsats_rankmotifs.out.re_match" />
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
249 </test>
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
250 <!-- Test with 454 input -->
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
251 <test>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
252 <param name="platform_type" value="454" />
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
253 <param name="input_fasta" value="454_in.fa" ftype="fasta" />
7
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
254 <expand macro="output_454_microsat_summary" />
5e133b7b79a6 Uploaded version 0.02.04.6 (uses conda dependency resolution).
pjbriggs
parents: 6
diff changeset
255 <output name="output_pal_summary" compare="re_match" file="454_microsats.out.re_match" />
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
256 </test>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
257 </tests>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
258 <help>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
259 .. class:: infomark
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
260
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
261 **What it does**
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
262
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
263 This tool runs the pal_finder program, which finds microsatellite repeat elements
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
264 directly from raw 454 or Illumina paired-end sequencing reads. It then designs PCR
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
265 primers to amplify these repeat loci (Potentially Amplifiable Loci: PAL).
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
266
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
267 Optionally for Illumina data, one or more filters can be applied to the output from
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
268 pal_finder to:
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
269
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
270 * Only include loci with designed primers
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
271 * Exclude loci where the primer sequences occur more than once in the reads
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
272 * Only include loci with 'perfect' motifs (and rank by motif size,largest to
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
273 smallest)
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
274 * Use PANDAseq to assemble paired-end reads and confirm primer sequences are
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
275 present in high-quality assembly
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
276
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
277 Pal_finder runs the primer3_core program; information on the settings used in
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
278 primer3_core can be found in the Primer3 manual at
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
279 http://primer3.sourceforge.net/primer3_manual.htm
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
280
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
281 -------------
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
282
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
283 .. class:: infomark
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
284
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
285 **Credits**
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
286
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
287 This Galaxy tool has been developed by Peter Briggs within the Bioinformatics Core
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
288 Facility at the University of Manchester. It runs the pal_finder package which can be
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
289 obtained from http://sourceforge.net/projects/palfinder/:
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
290
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
291 * PLoS One. 2012; 7(2): e30953 "Rapid Microsatellite Identification from Illumina Paired-End
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
292 Genomic Sequencing in Two Birds and a Snake" Todd A. Castoe, Alexander W. Poole, A. P.
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
293 Jason de Koning, Kenneth L. Jones, Diana F. Tomback, Sara J. Oyler-McCance, Jennifer A.
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
294 Fike, Stacey L. Lance, Jeffrey W. Streicher, Eric N. Smith, and David D. Pollock
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
295
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
296 The paper is available at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3279355/
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
297
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
298 This tool is compatible with pal_finder version 0.02.04, which in turn runs the
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
299 primer3_core program (version 2.0.0-alpha is required, available from
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
300 http://primer3.sourceforge.net/releases.php):
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
301
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
302 * Steve Rozen and Helen J. Skaletsky (2000) "Primer3 on the WWW for general users and for
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
303 biologist programmers". In: Krawetz S, Misener S (eds) Bioinformatics Methods and
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
304 Protocols: Methods in Molecular Biology. Humana Press, Totowa, NJ, pp 365-386
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
305
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
306 The paper is available at
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
307 http://purl.com/STEVEROZEN/papers/rozen-and-skaletsky-2000-primer3.pdf
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
308
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
309 The filtering and assembly of the pal_finder output for Illumina data is performed
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
310 using a Python utility written by Graeme Fox at the University of Manchester, and which
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
311 is included with this tool; this utility uses the BioPython and PANDAseq packages.
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
312
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
313 Please kindly acknowledge both this Galaxy tool, the pal_finder and primer3 packages, and
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
314 the utility script and its dependencies if you use it in your work.
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
315 </help>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
316 <citations>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
317 <!--
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
318 See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
319 Can be either DOI or Bibtex
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
320 Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
321 -->
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
322 <citation type="doi">10.1371/journal.pone.0030953</citation>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
323 <citation type="bibtex">@Article{pmid10547847,
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
324 Author="Rozen, S. and Skaletsky, H. ",
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
325 Title="{{P}rimer3 on the {W}{W}{W} for general users and for biologist programmers}",
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
326 Journal="Methods Mol. Biol.",
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
327 Year="2000",
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
328 Volume="132",
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
329 Pages="365--386",
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
330 URL="{http://purl.com/STEVEROZEN/papers/rozen-and-skaletsky-2000-primer3.pdf}"
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
331 }</citation>
2
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
332 <citation type="doi">10.1093/bioinformatics/btp163</citation>
b6ccc7dd7b02 Version 0.02.04.3.
pjbriggs
parents: 1
diff changeset
333 <citation type="doi">10.1186/1471-2105-13-31</citation>
0
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
334 </citations>
3f908e7fff4f Uploaded first version to toolshed.
pjbriggs
parents:
diff changeset
335 </tool>