Mercurial > repos > iuc > snp_sites

annotate snp-sites.xml @ 1:5804f786060d draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
author iuc
date Sat, 02 Nov 2019 11:12:17 -0400
parents efe8f0e53d3e
children
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efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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1 <?xml version='1.0' encoding='UTF-8'?>
1
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2 <tool id='snp_sites' name='Finds SNP sites' version='@TOOL_VERSION@+galaxy0'>
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efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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3 <description>from a multi-FASTA alignment file</description>
1
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4 <macros>
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5 <token name="@TOOL_VERSION@">2.5.1</token>
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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6 </macros>
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efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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7 <requirements>
1
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8 <requirement type='package' version='@TOOL_VERSION@'>snp-sites</requirement>
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efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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9 </requirements>
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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10 <version_command>snp-sites -V</version_command>
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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11 <command detect_errors='aggressive'><![CDATA[
1
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12 #if str($out_type.ot_select) == "alignment"
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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13 #if str($out_type.formats) == 'None'
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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14 echo "Error, no output format specified" >&2 && exit 1 ;
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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15 #set outputs=""
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16 #else
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17 #set outputs=" ".join(str($out_type.formats).split(","))
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18 #end if
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19 #end if
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20
0
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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21 snp-sites
1
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22 #if str($out_type.ot_select) == "alignment"
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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23 $outputs
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24 $out_type.b
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25 $out_type.c
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26 #else if str($out_type.ot_select) == "counts"
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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27 -C
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28 #end if
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29 -o output
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30 '$input_fasta'
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31
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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32 #if str($out_type.ot_select) == "counts"
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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33 && mv output $output_counts
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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34 #else if ',' in str($out_type.formats)
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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35 #if '-m' in str($out_type.formats)
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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36 && mv 'output.snp_sites.aln' '$output_fasta'
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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37 #end if
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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38 #if '-v' in str($out_type.formats)
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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39 && mv 'output.vcf' '$output_vcf'
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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40 #end if
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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41 #if '-p' in str($out_type.formats)
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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42 && mv 'output.phylip' '$output_phylip'
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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43 #end if
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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44 #else
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45 #if str($out_type.formats) == '-m'
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46 && mv 'output' '$output_fasta'
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47 #else if str($out_type.formats) == '-v'
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48 && mv 'output' '$output_vcf'
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49 #else if str($out_type.formats) == '-p'
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50 && mv 'output' '$output_phylip'
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51 #end if
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52 #end if
0
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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53 ]]></command>
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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54 <inputs>
1
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55
0
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56 <param name='input_fasta' format='fasta' type='data' label='FASTA file' />
1
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57 <conditional name="out_type" label="Output type">
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58 <param type="select" name="ot_select" label="Output">
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59 <option value="alignment" selected="true">Sequence alignment / VCF</option>
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60 <option value="counts">Constant site count (suitable for IQ-TREE -fconst)</option>
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61 </param>
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62 <when value="alignment">
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63 <param type='select' multiple='true' name='formats' label='Output formats' help='Output format to use if not counting constant sites'>
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64 <option value="-m" selected="true">Multi-FASTA alignment file</option>
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65 <option value="-v">VCF</option>
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66 <option value="-p">Phylip</option>
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67 </param>
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68 <param argument="-b" label="Output constant sites (suitable for use in BEAST)" truevalue="-b" falsevalue=""
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69 type="boolean" help="Output monomorphic (constant) as opposed to polymorphic (variable) sites"/>
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70 <param argument="-c" label="Only output columns containing exclusively ACTG" truevalue="-c" falsevalue=""
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71 type="boolean" help="Ignore columns containing ambiguous characters and gaps"/>
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72 </when>
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73 <when value="counts">
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74 </when>
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75 </conditional>
0
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76 </inputs>
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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77 <outputs>
1
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78 <data name='output_fasta' format='fasta' label='${tool.name} on ${on_string}: FASTA'>
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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79 <!-- this becomes a catch-all for when no format is specified. if no format is specified the job ends with an error but shows 1 red dataset output -->
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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80 <filter>(out_type["ot_select"] == "alignment" and out_type["formats"] is not None and '-m' in out_type["formats"]) or (out_type["ot_select"] == "alignment" and out_type.formats is None)</filter>
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81 </data>
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82 <data name='output_vcf' format='vcf' label='${tool.name} on ${on_string}: VCF' from_work_dir='output.vcf'>
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83 <filter>out_type["ot_select"] == "alignment" and out_type["formats"] is not None and '-v' in out_type["formats"]</filter>
5804f786060d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit e4222f6179041846870721bfcb4d8e587ead8d8f"
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84 </data>
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85 <data name='output_phylip' format='phylip' label='${tool.name} on ${on_string}: phylip'>
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86 <filter>out_type["ot_select"] == "alignment" and out_type["formats"] is not None and '-p' in out_type["formats"]</filter>
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87 </data>
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88 <data name='output_counts' format='tabular' label='${tool.name} on ${on_string}: constant site counts'>
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89 <filter>out_type["ot_select"] == "counts"</filter>
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90 </data>
0
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91 </outputs>
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92 <tests>
1
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93 <test expect_num_outputs="3">
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94 <param name='input_fasta' value='input.fasta' ftype='fasta' />
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95 <conditional name="out_type">
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96 <param name="ot_select" value="alignment" />
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97 <param name='formats' value='-m,-p,-v' />
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98 </conditional>
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99 <output name='output_fasta' value='output.fasta' ftype='fasta' />
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100 <output name='output_vcf' value='output.vcf' ftype='vcf' />
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101 <output name='output_phylip' value='output.phylip' ftype='phylip' />
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102 </test>
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103 <test expect_num_outputs="1">
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104 <param name='input_fasta' value='input.fasta' ftype='fasta' />
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105 <conditional name="out_type">
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106 <param name="ot_select" value="alignment" />
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107 <param name='formats' value='-m' />
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108 <param name='b' value='True' />
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109 </conditional>
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110 <output name='output_fasta' value='output_monomorphic.fasta' ftype='fasta' />
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111 </test>
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112 <test expect_num_outputs="1">
0
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113 <param name='input_fasta' value='input.fasta' ftype='fasta' />
1
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114 <conditional name="out_type">
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115 <param name="ot_select" value="alignment" />
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116 <param name='formats' value='-m' />
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117 <param name='c' value='True' />
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118 </conditional>
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119 <output name='output_fasta' value='output_actg.fasta' ftype='fasta' />
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120 </test>
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121 <test expect_num_outputs="1">
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122 <param name='input_fasta' value='input.fasta' ftype='fasta' />
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123 <conditional name="out_type">
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124 <param name="ot_select" value="alignment" />
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125 <param name='formats' value='-m' />
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126 <param name='b' value='True' />
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127 <param name="c" value="True" />
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128 </conditional>
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129 <output name='output_fasta' value='output_monomorphic_actg.fasta' ftype='fasta' />
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130 </test>
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131 <test expect_num_outputs="1">
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132 <param name='input_fasta' value='input.fasta' ftype='fasta' />
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133 <conditional name="out_type">
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134 <param name="ot_select" value="counts" />
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135 <param name='C' value='True' />
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136 </conditional>
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137 <output name='output_counts' value='output_counts.tabular' ftype='tabular' />
0
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138 </test>
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139 </tests>
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140 <help>
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141 <![CDATA[
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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142
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143 **SNP-sites**
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144
1
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145 This tool can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers.
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146 SNP-sites is implemented in C and is available under the open source license GNU GPL version 3.
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147
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148 Alternatively it can report on the number of constant sites in an alignment in a format (A count, C count, G count, T count) suitable for passing
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149 to IQ-TREE's `-fconst` option.
0
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150
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151 **Input FASTA format:**
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152
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153 The first sequence will be taken as a reference.
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154
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155 .. code-block::
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156
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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157 >sample1
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158 AGACACAGTCAC
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159
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160 >sample1
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161 AGACAC----AC
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162
efe8f0e53d3e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/snp-sites commit 3a0370239dd8ee753194be5c580b1d9b8ec98bee
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163 >sample1
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164 AAACGCATTCAN
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165
1
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166 **Options**
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167
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168 In addition to the default output mode, this tool supports three other options:
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169
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170 1. Output only constant (monomorphic) (i.e. not polymorphic) sites (useful for input to BEAST)
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171
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172 2. Output only columns that have purely ACTGs in them (i.e. no gaps or ambiguous nucleotides). This can be used together with the previous option.
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173
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174 3. Output only a count of constant sites, in a format suitable for use with IQ-TREE `-fconst`. This option cannot be used together with the previously mentioned options.
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175
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176 **Output files:**
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177
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178 The output of the tool are three different files in following format:
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179
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180 - a multi fasta alignment,
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181 - relaxed phylip format and,
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182 - VCF.
1
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183 - alternatively constant site counts (As, Cs, Gs and Ts).
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184
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185 The VCF file for the above specified input is
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186
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187 The output of the tool are three different files in following format:
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188
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189 - a multi fasta alignment,
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190 - relaxed phylip format and,
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191 - VCF.
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192
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193 The VCF file for the above specified input is
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194
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195 ===== === == === === ==== ====== ==== ====== ======= ======= =======
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196 CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample1 sample1 sample1
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197 ----- --- -- --- --- ---- ------ ---- ------ ------- ------- -------
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198 1 2 . G A . . . GT 0 0 1
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199 ----- --- -- --- --- ---- ------ ---- ------ ------- ------- -------
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200 1 5 . A G . . . GT 0 0 1
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201 ----- --- -- --- --- ---- ------ ---- ------ ------- ------- -------
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202 1 8 . G .,T . . . GT 0 1 2
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203 ===== === == === === ==== ====== ==== ====== ======= ======= =======
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204
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205 Thus the tool identified three variations (SNPs): in 2nd, 5th, and 8th positions (A instead of G, G instead of A, and unknown nucleotide or T instead of G, respectively).
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206
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207
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208 ]]>
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209 </help>
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210 <citations>
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211 <citation type="doi">10.1099/mgen.0.000056</citation>
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212 </citations>
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213 </tool>