Mercurial > repos > iuc > cooc_mutbamscan

annotate cooc_mutbamscan.xml @ 0:90d4dfb2d266 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
author iuc
date Thu, 11 Aug 2022 13:48:28 +0000
parents
children df723877bcd8
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0
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1 <tool id="cooc_mutbamscan" name="Cojac: mutbamscan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
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2 profile="@PROFILE@">
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3 <description>
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4 scan an alignment file for mutation co-occurrences
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5 </description>
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6 <macros>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="biotools"/>
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10 <expand macro="requirements"/>
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11 <expand macro="version"/>
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12 <command detect_errors="exit_code"><![CDATA[
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13 ln -s '$bed_file' 'bed_file' &&
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14 @VOCDIR_COMMAND@
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15 #import re
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16 #set identifier = re.sub('[^\s\w\-\\.]', '_', str($bam_file.element_identifier))
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17 ln -s '$bam_file' ${identifier}.bam &&
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18 ln -s '${bam_file.metadata.bam_index}' ${identifier}.bai &&
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19 cooc-mutbamscan
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20 -a '${identifier}.bam'
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21 -b 'bed_file'
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22 -m '$vocdir'
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23 -y cooc.yaml
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24 -j cooc.json
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25 #if $amplicons_file.choice == 'build'
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26 -A amplicons.yaml
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27 #else
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28 -Q '$amplicons_file.in_amp'
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29 #end if
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30 -t cooc.tsv
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31 --cooc $cooc
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32 ]]></command>
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33 <inputs>
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34 <expand macro="vocdir_input"/>
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35 <param name="bed_file" type="data" format="bed"
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36 label="BED file defining the amplicons"/>
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37 <param name="bam_file" type="data" format="bam,cram,sam"
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38 label="Alignment BAM/CRAM/SAM file"/>
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39 <param argument="--cooc" type="integer" min="1" value="2"
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40 label="Minimum number of cooccurence mutations on the same amplicon"/>
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41 <conditional name="amplicons_file">
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42 <param name="choice" type="select" label="Source of amplicons YAML file">
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43 <option value="build">Build from BED + set of YAMLs for variants of concern</option>
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44 <option value="custom">From history</option>
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45 </param>
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46 <when value="build"/>
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47 <when value="custom">
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48 <param name="in_amp" type="data" format="yaml"
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49 label="YAML file to query amplicons"/>
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50 </when>
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51 </conditional>
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52 <param name="output_files" type="select" display="checkboxes"
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53 multiple="true" label="Output files">
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54 <option value="yaml" selected="true">YAML</option>
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55 <option value="json">JSON</option>
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56 <option value="tabular">tabular</option>
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57 </param>
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58 </inputs>
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59 <outputs>
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60 <data name="cooc_yaml" format="yaml"
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61 label="${tool.name} on ${on_string}: Mutation cooccurrence (yaml)"
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62 from_work_dir="cooc.yaml">
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63 <filter>'yaml' in output_files</filter>
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64 </data>
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65 <data name="cooc_json" format="json"
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66 label="${tool.name} on ${on_string}: Mutation cooccurrence (json)"
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67 from_work_dir="cooc.json">
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68 <filter>'json' in output_files</filter>
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69 </data>
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70 <data name="cooc_tsv" format="tabular"
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71 label="${tool.name} on ${on_string}: Mutation cooccurrence (tabular)"
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72 from_work_dir="cooc.tsv">
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73 <filter>'tabular' in output_files</filter>
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74 </data>
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75 <data name="amplicons" format="yaml"
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76 label="${tool.name} on ${on_string}: Amplicons (yaml)"
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77 from_work_dir="amplicons.yaml">
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78 <filter>amplicons_file['choice'] == 'build'</filter>
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79 </data>
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80 </outputs>
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81 <tests>
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82 <!-- Test 1: build yaml for amplicons from bed and voc/ -->
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83 <test expect_num_outputs="4">
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84 <conditional name="vocdir_option">
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85 <param name="choice" value="custom"/>
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86 <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
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87 </conditional>
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88 <param name="bam_file" value="tbam11.bam"/>
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89 <param name="bed_file" value="nCoV-2019.insert.V3.bed"/>
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90 <conditional name="amplicons_file">
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91 <param name="choice" value="build"/>
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92 </conditional>
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93 <param name="output_files" value="yaml,json,tabular"/>
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94 <output name="cooc_yaml" ftype="yaml">
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95 <assert_contents>
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96 <has_text text="76_om1"/>
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97 <has_text text="81_om1"/>
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98 </assert_contents>
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99 </output>
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100 <output name="cooc_json" ftype="json">
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101 <assert_contents>
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102 <has_text text="76_om1"/>
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103 <has_text text="81_om1"/>
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104 </assert_contents>
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105 </output>
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106 <output name="cooc_tsv" ftype="tabular">
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107 <assert_contents>
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108 <has_text text="76_om1"/>
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109 <has_text text="81_om1"/>
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110 </assert_contents>
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111 </output>
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112 <output name="amplicons" ftype="yaml">
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113 <assert_contents>
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114 <has_text text="76_om1"/>
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115 <has_text text="81_om1"/>
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116 </assert_contents>
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117 </output>
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118 </test>
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119 <!-- Test 2: supply yaml for amplicons and voc/ from cache -->
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120 <test expect_num_outputs="2">
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121 <conditional name="vocdir_option">
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122 <param name="choice" value="cache"/>
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123 </conditional>
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124 <param name="bam_file" value="tbam11.bam"/>
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125 <param name="bed_file" value="nCoV-2019.insert.V3.bed"/>
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126 <conditional name="amplicons_file">
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127 <param name="choice" value="custom"/>
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128 <param name="in_amp" value="amplicons111.yaml"/>
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129 </conditional>
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130 <param name="output_files" value="yaml,tabular"/>
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131 <output name="cooc_yaml" ftype="yaml">
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132 <assert_contents>
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133 <has_text text="76_om1"/>
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134 <has_text text="81_om1"/>
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135 </assert_contents>
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136 </output>
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137 <output name="cooc_tsv" ftype="tabular">
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138 <assert_contents>
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139 <has_text text="76_om1"/>
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140 <has_text text="81_om1"/>
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141 </assert_contents>
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142 </output>
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143 </test>
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144 </tests>
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145 <help><![CDATA[
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146 @HELP_HEADER@
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147
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148 Information about **cooc-mutbamscan** method
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149 ============================================
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150
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151 The method scans an alignment BAM/CRAM/SAM file for mutation co-occurrences and output a JSON or YAML file.
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152
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153 ]]></help>
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154 <expand macro="citations"/>
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155 </tool>