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