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1 <tool id="affr2vcf" name="Convert Affymetrix" version="1.9">
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2 <description>genotype calls and intensities to VCF</description>
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3 <requirements>
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4 <requirement type="package" version="1.9">bcftools-gtc2vcf-plugin</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code"><![CDATA[
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7 #set text_outputs_dir = 'text_outputs'
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8
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8 export BCFTOOLS_PLUGINS=\$(dirname `which bcftools`)/../libexec/bcftools &&
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4
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9 mkdir $text_outputs_dir &&
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9
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10 bcftools +\$BCFTOOLS_PLUGINS/affy2vcf.so
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7
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11 #if str($reference_genome_source_cond.reference_genome_source) == "history":
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10
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12 --fasta-ref '$reference_genome_source_cond.history_item'
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7
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13 #else:
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10
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14 --fasta-ref '$reference_genome_source_cond.locally_cached_item'
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7
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15 #end if
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16 --annot '$annot'
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12
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17 --snp-posteriors '$snp_posteriors'
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18 --summary '$summary'
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19 --report '$report'
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20 --calls '$calls'
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21 --confidences '$confidences'
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22 #if str($output_gender_estimate_cond.output_gender_estimate) == "yes"
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23 --sex '$output_gender_estimate'
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24 #end if
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25 #if str($append_version) == "no":
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26 --no-version
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27 #end if
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28 --output '$output'
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11
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29 --output-type $output_type
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30 --threads \${GALAXY_SLOTS:-4}
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31 ]]></command>
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32 <inputs>
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13
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33 <param name="annot" type="data" format="csv" label="Probeset annotation file" />
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34 <param name="summary" type="data" format="txt" label="Apt-probeset genotype summary file" />
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35 <param name="snp_posteriors" type="data" format="txt" label="Apt-probeset genotype snp-posteriors file" />
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36 <param name="report" type="data" format="txt" label="Apt-probeset genotype report file" />
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37 <param name="confidences" type="data" format="txt" label="Apt-probeset genotype confidences file" />
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38 <param name="calls" type="data" format="txt" label="Apt-probeset genotype calls file" />
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39 <conditional name="reference_genome_source_cond">
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40 <param name="reference_genome_source" type="select" label="Choose the source for the reference genome">
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41 <option value="history" selected="true">Use a reference genome from my history</option>
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42 <option value="cached">Use a locally cached genome index</option>
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43 </param>
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44 <when value="history">
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45 <param name="history_item" type="data" format="fasta" label="Select reference genome" />
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5
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46 </when>
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47 <when value="cached">
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48 <param name="locally_cached_item" type="select" format="fasta" label="Fasta reference sequence">
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49 <options from_data_table="all_fasta">
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50 <column name="name" index="1"/>
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51 <column name="value" index="2"/>
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52 <column name="path" index="2"/>
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53 <filter type="sort_by" column="1"/>
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54 <validator type="no_options" message="No cached Fasta genome references are available for the build associated with the selected probeset annotation file." />
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5
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55 </options>
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56 </param>
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57 </when>
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58 </conditional>
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12
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59 <conditional name="output_gender_estimate_cond">
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60 <param name="output_gender_estimate" type="select" force_select="true" label="Output apt-probeset-genotype gender estimate?">
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61 <option value="no" selected="true">No</option>
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62 <option value="yes">Yes</option>
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63 </param>
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64 <when value="no"/>
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65 <when value="yes"/>
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66 </conditional>
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67 <param name="append_version" type="select" force_select="true" label="Append version and command line to the header?">
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68 <option value="no" selected="true">No</option>
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69 <option value="yes">Yes</option>
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70 </param>
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71 <param name="output_type" type="select" force_select="true" label="Select format for output">
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72 <option value="v" selected="true">Uncompressed VCF</option>
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73 <option value="z">Compressed VCF</option>
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74 <option value="u" selected="true">Uncompressed BCF</option>
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75 <option value="b">Compressed BCF</option>
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76 </param>
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77 </inputs>
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78 <outputs>
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79 <data name="output" format="vcf" />
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80 <data name="output_gender_estimate" format="txt" label="${tool.name} (gender estimate) on ${on_string}">
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81 <filter>output_gender_estimate_cond['output_gender_estimate'] == "yes"</filter>
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82 </data>
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4
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83 </outputs>
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84 <tests>
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85 <test>
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12
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86 <param name="reference_genome_source" value="history"/>
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87 <param name="history_item" value="sub50_adig_genome.fasta" ftype="fasta"/>
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88 <param name="annot" value="axiom_acropsnp_coral_annotation.r1.csv" ftype="csv"/>
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89 <param name="summary" value="sub50_axiomgt1.summary.txt" ftype="txt"/>
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90 <param name="snp_posteriors" value="sub50_axiomgt1.snp_posteriors.txt" ftype="txt"/>
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91 <param name="report" value="axiomgt1.report.txt" ftype="txt"/>
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92 <param name="confidences" value="sub50_axiomgt1.confidences.txt" ftype="txt"/>
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93 <param name="calls" value="sub50_axiomgt1.calls.txt" ftype="txt"/>
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94 <output name="output" value="output.vcf" ftype="vcf"/>
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95 </test>
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96 </tests>
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97 <help>
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98 This tool converts Affymetrix genotype calls and intensity files to VCF format.
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99
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100 -----
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101
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102 **Required options**
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103
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104 * **Probeset annotation file** - probeset annotation file produced by the sequencing run.
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105 * **Apt-probeset genotype summary file** - apt-probeset genotype summary file produced by the sequencing run.
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106 * **Apt-probeset genotype snp-posteriors file** - apt-probeset genotype snp-posteriors file produced by the sequencing run.
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107 * **Apt-probeset genotype report file** - apt-probeset genotype report file produced by the sequencing run.
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108 * **Apt-probeset genotype confidences file** - apt-probeset genotype confidences file produced by the sequencing run.
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109 * **Apt-probeset genotype calls file** - apt-probeset genotype calls file produced by the sequencing run.
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110 * **Choose the source for the reference genome** - select a reference genome from your history or one installed into your local Galaxy environment by a data manager tool.
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111
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112 **Other options**
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113
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114 * **Output apt-probeset-genotype gender estimate** - output apt-probeset-genotype gender estimate into an additional dataset.
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115 * **Append version and command line to the header** - append version and command line to the header of the output VCF dataset.
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116 * **Select format for output** - select one of uncompressed/compressed VCF/BCF.
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117 </help>
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118 <citations>
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119 <citation type="bibtex">
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120 @misc{None,
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121 journal = {None},
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122 author = {Genovese, Giulio},
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123 title = {None},
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124 year = {None},
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125 url = {https://github.com/freeseek/gtc2vcf},}
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126 </citation>
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127 </citations>
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128 </tool>
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