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"planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
author nml
date Tue, 24 Mar 2020 13:27:46 -0400
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33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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1 <tool id="pneumocat" name="PneumoCaT" version="@VERSION@">
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2 <description> Pneumococcal Capsular Typing of illumina reads</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" />
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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7 <command detect_errors="exit_code">
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8 <![CDATA[
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9
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10 #import os
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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11 #import re
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33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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13 #def check_ending($name, $forward_read=True)
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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14 ## Pneumocat needs to have name_1.fastq and name_2.fastq to work
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15 ## Check for correct ending and change ending if needed
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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16
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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17 #if re.search(r'(\.|_)\S*(1|2)*$', $name)
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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18 #if $forward_read
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19 #return re.sub(r'(\.|_)\S*(1|2)*$', '_R1.fastq', $name)
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20 #else
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21 #return re.sub(r'(\.|_)\S*(1|2)*$', '_R2.fastq', $name)
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22 #end if
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23
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24 #else
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25 #if $forward_read
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26 #return '{}_R1.fastq'.format($name)
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27 #else
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28 #return '{}_R2.fastq'.format($name)
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29 #end if
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30 #end if
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31 #end def
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32
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33
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34 #if $input.type == 'paired'
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35 #set $initial = re.sub('[^\w_]', '_', os.path.splitext($input.forward.name)[0])
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36
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37 #set $for_input = $check_ending($initial)
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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38 #set $rev_input = $check_ending($initial, forward_read=False)
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39
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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40 ln -s '$input.forward' ./$for_input &&
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41 ln -s '$input.reverse' ./$rev_input &&
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42
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43 #elif $input.type == 'paired_collection'
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44 #set $initial = re.sub('[^\w_]', '_', os.path.splitext($input.fastq_collection.forward.name)[0])
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45
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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46 #set $for_input = $check_ending($initial)
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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47 #set $rev_input = $check_ending($initial, forward_read=False)
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48
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49 ln -s '$input.fastq_collection.forward' ./$for_input &&
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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50 ln -s '$input.fastq_collection.reverse' ./$rev_input &&
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51
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52 #end if
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53
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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54 PneumoCaT.py -1 '$for_input' -2 '$rev_input' -o outputs --threads '\${GALAXY_SLOTS:-1}' --cleanup
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55 ]]>
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56 </command>
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57 <inputs>
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58 <conditional name="input">
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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59 <param name="type" type="select" label="Sequence Data Type">
33de0245ed99 "planemo upload for repository https://github.com/phe-bioinformatics/PneumoCaT commit c1002f7ad15e676357c6489878291de07bbde841"
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60 <option value="paired">Paired-end reads (FASTQ)</option>
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61 <option value="paired_collection">Paired-end reads collection (FASTQ)</option>
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62 </param>
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63 <when value="paired">
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64 <param name="forward"
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65 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
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66 optional="false"
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67 multiple="false"
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68 label="Forward reads (FASTQ)"
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69 help="Must have ASCII encoded quality scores"
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70 />
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71 <param name="reverse"
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72 type="data" format="fastq,fastqsanger,fastq.gz,fastqsanger.gz"
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73 optional="false"
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74 label="Reverse reads (FASTQ)"
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75 help="File format must match the Forward FASTQ file"
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76 />
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77 </when>
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78 <when value="paired_collection">
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79 <param name="fastq_collection"
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80 type="data_collection" format="fastq,fastqsanger, fastq.gz, fastqsanger.gz"
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81 collection_type="paired"
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82 optional="false"
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83 label="Paired-end reads collection (FASTQ)"
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84 />
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85 </when>
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86 </conditional>
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87 </inputs>
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88 <outputs>
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89 <data format="txt" name="coverage_summary" from_work_dir="outputs/coverage_summary.txt" label="PneumoCaT Coverage Summary.txt"/>
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90 <data format="xml" name="results" from_work_dir="outputs/*.results.xml" label="PneumoCaT Results.xml"/>
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91 <data format="xml" name="specific_results" from_work_dir="outputs/SNP_based_serotyping/*.results.xml" label="PneumoCaT Serotype Distinction.xml"/>
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92 <data format="txt" name="variant_summary" from_work_dir="outputs/SNP_based_serotyping/variant_summary.yml" label="PneumoCaT Variant Summary.yml"/>
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93 </outputs>
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94 <tests>
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95 <test>
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96 <conditional name="input">
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97 <param name="type" value="paired" />
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98 <param name="forward" value="09N_R1.fastq" />
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99 <param name="reverse" value="09N_R2.fastq" />
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100 </conditional>
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101 <output name="coverage_summary" file="coverage_summary.txt" />
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102 <output name="results" file="results.xml" />
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103 </test>
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104 <test>
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105 <conditional name="input">
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106 <param name="type" value="paired_collection" />
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107 <param name="fastq_collection">
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108 <collection type="paired">
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109 <element name="forward" value="09N_R1.fastq.gz" ftype="fastq.gz" />
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110 <element name="reverse" value="09N_R2.fastq.gz" ftype="fastq.gz" />
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111 </collection>
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112 </param>
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113 </conditional>
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114 <output name="coverage_summary" file="coverage_summary.txt" />
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115 <output name="results" file="results.xml" />
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116 </test>
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117 </tests>
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118 <help>
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119 <![CDATA[
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120
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121 PneumoCaT
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122 ---------
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123
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124 PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to
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125 S.pneumoniae genomic data (Illumina). More info can be found at the `PneumoCaT github page <https://github.com/phe-bioinformatics/PneumoCaT>`_
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126
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127 Program Steps
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128 #############
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129
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130 - **Step 1:** Reads from each readset are mapped to capsular locus sequences for all known capsular types using bowtie2
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131
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132 - This step is considered successful if the readset matches > 90% to one or more capsular locus sequences
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133
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134 - If only a singular capsular locus is matched, PneumoCaT terminates and reports that as the assigned capsular type
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135
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136 - If more than 1 loci are matched then the tool moves to step 2
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137
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138 - **Step 2:** Variant calling with the capsular type variant database
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139
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140 - Used to distinguish serotypes within a serogroup/genogroup
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141
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142 Please note PneumoCaT applies a quality metric requiring a mean depth of 20 reads across the mapped sequence
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143 and a minimum depth of 5 reads for mapping. The report will retrun "Failed" if these conditions are not met.
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144
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145 Inputs
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146 ######
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147
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148 - **Paired-end Illumina reads** with one of the following example formats is prefered:
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149
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150 - <name>_1.fastq and <name>_2.fastq
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151
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152 - <name>_R1.fastq and <name>_R2.fastq
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153
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154 - <name>_R1.fastqsanger.gz and <name>_R2.fastqsanger.gz
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155
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156 - If the reads are not formatted as above, the wrapper will append _R1.fastq and _R2.fastq to allow function
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157
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158 Outputs
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159 #######
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160
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161 Please see `**PneumoCaTs interpreting results document** <https://github.com/phe-bioinformatics/PneumoCaT/blob/master/Documentation/InterpretingResults.pdf>`_
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162 for full up-to-date information on how to interpret PneumoCaT results.
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163
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164 Galaxy will output 4 results running PneumoCaT with 2 of the results only appearing if **Step 2** variant calling is done
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165
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166 **1. Coverage Summary.txt** -- Always output unless fails --
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167
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168 **2. Results.xml** -- Always output unless fails --
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169
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170 **3. Serotype distinction.xml** -- Step 2 Required --
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171
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172 **4. Variant Summary.txt** -- Step 2 Required --
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173
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174
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175 **Note** - Galaxy will always output files 3 and 4 even if step 2 is not done. In these cases, the files will have no data.
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176
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177 ]]>
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178 </help>
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179 <expand macro="citations" />
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180 </tool>