Mercurial > repos > iuc > medaka_snp

annotate snp.xml @ 1:630e6aeeb7e8 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7105600c6ba7a49e8933e1a1357566fc2126df58
author iuc
date Tue, 26 Sep 2023 10:11:25 +0000
parents 179342c7b86c
children
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179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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1 <tool id="medaka_snp" name="medaka SNP tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>decodes probabilities to SNPs</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 ## initialize
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10 @REF_FASTA@
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11
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12
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13 #if $pool.pool_mode == "Yes":
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14 ## run
179342c7b86c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 4d3dfd4bcb567178107dcfd808ff03f9fec0bdbd
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15 medaka snp
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16 ## optional
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17 --debug
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18 #if $regions
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19 --regions '${regions}'
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20 #end if
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21 --threshold $threshold
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22 #if $ref_vcf
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23 --ref_vcf '$ref_vcf'
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24 #end if
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25 $verbose
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26 ## required
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27 reference.fa
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28 #for $current in $pool.inputs
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29 '$current'
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30 #end for
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31 #elif $pool.pool_mode == "No":
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32 ## run
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33 medaka snp
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34 ## optional
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35 --debug
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36 #if $regions
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37 --regions '${regions}'
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38 #end if
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39 --threshold $threshold
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40 #if $ref_vcf
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41 --ref_vcf '$ref_vcf'
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42 #end if
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43 $verbose
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44 ## required
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45 reference.fa
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46 '$pool.input'
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47 #end if
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48 #if str($output_annotated.output_annotated_select) == 'false':
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49 '$out_SNPs' ##output
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50 2>&1 | tee '$out_log'
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51 #else
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52 raw.vcf ##output of medaka snp
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53 2>&1 | tee '$out_log'
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54 && ln -s '$output_annotated.in_bam' in.bam
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55 && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
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56 && medaka tools annotate --dpsp --pad $output_annotated.pad raw.vcf reference.fa in.bam tmp.vcf
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57 && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_SNPs'
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58 #end if
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59 ]]></command>
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60 <inputs>
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61 <conditional name="pool">
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62 <param name="pool_mode" type="select" label="Are you pooling HDF5 datasets?">
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63 <option value="No" selected="true">No</option>
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64 <option value="Yes">Yes</option>
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65 </param>
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66 <when value="Yes">
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67 <param name="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
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68 </when>
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69 <when value="No">
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70 <param name="input" type="data" format="h5" label="Select consensus file(s)"/>
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71 </when>
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72 </conditional>
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73 <expand macro="reference"/>
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74 <param argument="--regions" type="text" value="" optional="true" label="Set reference names to limit SNP calling" help="Separated by ','.">
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75 <sanitizer invalid_char="">
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76 <valid initial="string.ascii_letters,string.digits">
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77 <add value="_"/>
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78 <add value=","/>
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79 <add value="."/>
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80 </valid>
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81 </sanitizer>
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82 </param>
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83 <param argument="--threshold" type="float" label="Threshold for considering secondary calls" value="0.04" min="0" max="1" help="A value of 1 will result in haploid decoding" optional="true"/>
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84 <param name="ref_vcf" type="data" format="vcf" optional="true" label="Reference vcf"/>
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85 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
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86 <conditional name="output_annotated">
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87 <param name="output_annotated_select" type="select"
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88 label="Type of VCF to generate"
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89 help="SNP INFO fields in the VCF can be extended to include allele frequency, depth of coverage, etc., but this requires a BAM dataset to calculate those values from.">
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90 <option value="true" selected="true">Write annotated VCF with extended INFO</option>
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91 <option value="false">Write original decoded VCF with minimal INFO field</option>
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92 </param>
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93 <when value="true">
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94 <param name="in_bam" type="data" format="bam" optional="false" label="BAM to caclulate additional INFO fields from"/>
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95 <param name="pad" type="integer" min="1" value="25"
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96 label="Padding width on either side of SNP for realignment"
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97 help="To calculate the additional INFO fields the tool will run medaka tools anntotate, which performs local realignment of the region +- this width around each SNP. All calculated new fields will depend on the width chosen, so only change this value if you know what you are doing." />
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98 </when>
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99 <when value="false"/>
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100 </conditional>
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101 <param name="output_log_bool" type="boolean" label="Output log file?" checked="true"/>
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102 </inputs>
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103 <outputs>
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104 <data name="out_SNPs" format="vcf" label="${tool.name} on ${on_string}: called SNPs"/>
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105 <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
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106 <filter>output_log_bool</filter>
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107 </data>
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108 </outputs>
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109 <tests>
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110 <!--No annotation or log-->
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111 <test expect_num_outputs="1">
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112 <conditional name="pool">
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113 <param name="pool_mode" value="No"/>
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114 <param name="input" value="medaka_test.hdf"/>
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115 </conditional>
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116 <conditional name="reference_source">
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117 <param name="reference_source_selector" value="history"/>
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118 <param name="ref_file" value="ref.fasta"/>
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119 </conditional>
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120 <conditional name="output_annotated">
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121 <param name="output_annotated_select" value="false"/>
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122 </conditional>
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123 <param name="output_log_bool" value="false"/>
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124 <output name="out_SNPs">
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125 <assert_contents>
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126 <has_n_lines n="7"/>
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127 <has_line line="##fileformat=VCFv4.1" />
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128 <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
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129 </assert_contents>
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130 </output>
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131 </test>
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132 </tests>
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133 <help><![CDATA[
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134 .. class:: infomark
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135
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136 **What it does**
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137
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138 @WID@
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139
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140 This module decodes probabilities to SNPs but NOT indels.
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141
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142 For a more general solution see the medaka *variant* tool.
1
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143
0
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144 ----
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145
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146 .. class:: infomark
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147
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148 **Input**
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149
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150 - reference sequence (FASTA)
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151 - (several) consensus files (H5/HDF)
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152
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153 ----
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154
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155 .. class:: infomark
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156
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157 **Output**
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158
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159 - decoded SNP probabilities (VCF)
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160
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161 ----
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162
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163 .. class:: infomark
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164
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165 **References**
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166
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167 @REFERENCES@
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168 ]]></help>
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169 <expand macro="citations"/>
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170 </tool>