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"planemo upload for repository https://github.com/nebiolabs/tasmanian-mismatch commit d67025e9c7764d77f3f622b4d1ac0535b06c63de"
author iuc
date Sat, 24 Jul 2021 17:47:35 +0000
parents bc0b40dec7d2
children
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b15fbf90db53 "planemo upload for repository https://github.com/nebiolabs/tasmanian-mismatch commit d67025e9c7764d77f3f622b4d1ac0535b06c63de"
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1 <tool id="tasmanian_mismatch" name="Analysis of artifacts with Tasmanian" version="@TOOL_VERSION@" profile="20.05">
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2 <description>Quantify, visualize and summarize mismatches in deep sequencing data</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.0.7</token>
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5 <token name="@SAMTOOLS_VERSION@">1.13</token>
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6 </macros>
0
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7 <requirements>
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8 <requirement type="package" version="@TOOL_VERSION@">tasmanian-mismatch</requirement>
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9 <requirement type="package" version="@SAMTOOLS_VERSION@">samtools</requirement>
0
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10 </requirements>
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11 <command detect_errors="exit_code">
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12 <![CDATA[
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14 #set $reference_fasta_filename = "localref.fa"
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16 #if str( $reference_source.reference_source_selector ) == "history":
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17 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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18 #else:
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19 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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20 #end if
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22 samtools view '${bam_input}' |
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24 #if $bed_filename
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25 run_intersections -b '$bed_filename' |
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26 #end if
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28 run_tasmanian
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29 -q '${basequality}'
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30 -s '${softclips}'
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31 -m '${mapquality}'
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32 -c '${confidence}'
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33 -r '${reference_fasta_filename}' > '${output_table}'
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34
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35 ]]></command>
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36 <inputs>
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37 <!-- Bam alignment file -->
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38 <param type="data" name="bam_input" label="Bam/Sam alignemnt file" format="bam" help="Specify BAM/SAM dataset. If not using a bed file, this file MUST BE SORTED"/>
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39 <!-- reference genome upload -->
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40 <conditional name="reference_source">
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41 <param name="reference_source_selector" type="select" label="Reference genome" help="You can select a reference genome from your history or use a built-in index (Local cache)">
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42 <option value="cached">Local cache</option>
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43 <option value="history">History</option>
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44 </param>
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45 <when value="cached">
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46 <param name="ref_file" type="select" label="Select the reference genome from the list">
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47 <options from_data_table="all_fasta">
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48 <filter type="sort_by" column="2" />
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49 <validator type="no_options" message="No indexes are available" />
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50 </options>
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51 </param>
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52 </when>
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53 <when value="history">
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54 <param name="ref_file" type="data" format="fasta" label="Use reference genome from history" help="You can first upload a FASTA sequence to the history" />
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55 </when>
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56 </conditional>
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57
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58 <!-- bed file -->
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59 <param name="bed_filename" type="data" format="bed" optional="true" label="Select a bed file" help="The bed file should contain at least: &quot;chrN&quot;, &quot;start&quot; and &quot;stop&quot;, and is tab separated."/>
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60
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61 <!-- Additional parameters -->
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62 <param name="confidence" label="Boundary" type="integer" value="20" min="0" max="100"
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63 help="Number of bases in boundary region, from 0 to length of the read (read help below). Default=20"/>
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64 <param name="softclips" label="Choose an action with softclips" type="select" display="radio"
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65 help="How sofclips whould be treated. Values include 0,1 or 2 (read the help below). Default=0">
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66 <option value="1">Never use softcliped bases</option>
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67 <option value="2">Always use softcliped bases</option>
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68 <option value="0" selected="True">Automatic desicion (Default)</option>
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69 </param>
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70 <param name="mapquality" label="Map quality" type="integer" min="0" max="70" value="20" help="Exclude reads with lower mapQ than this number. Default=20"/>
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71 <param name="basequality" label="Base quality" type="integer" min="0" max="70" value="20" help="Exclude bases with lower Base quality than this number. Default=20"/>
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72 <param name="keepHTML_conditional" type="select" label="keep HTML output file?">
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73 <option value="yes">Yes</option>
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74 <option value="no">No</option>
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75 </param>
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76 </inputs>
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77
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78 <outputs>
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79 <data name="output_table" format="txt" />
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80 <data format="html" name="html_file" from_work_dir="Tasmanian_artifact_report.html" label="tasmanian-mismatch results table">
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81 <filter>keepHTML_conditional == "yes"</filter>
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82 </data>
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83 </outputs>
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84
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85 <tests>
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86 <!-- test when reference from history with bed-->
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87 <test>
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88 <param name="bam_input" value="test2.bam" ftype="bam"/>
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89 <param name="reference_source_selector" value="history"/>
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90 <param name="ref_file" value="small_region.fa"/>
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91 <param name="bed_filename" value="test2.bed" ftype="bed"/>
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92 <output name="output_table" file="test2-bed.output" lines_diff="4"/>
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93 </test>
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94 <!-- test when reference from history without bed-->
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95 <test>
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96 <param name="bam_input" value="test2.bam" ftype="bam"/>
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97 <param name="reference_source_selector" value="history"/>
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98 <param name="ref_file" value="small_region.fa"/>
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99 <output name="output_table" file="test2-nobed.output" lines_diff="4"/>
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100 </test>
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101 <!-- test when reference from cached-->
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102 <test>
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103 <param name="bam_input" value="test2.bam" ftype="bam" dbkey="hg38"/>
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104 <param name="reference_source_selector" value="cached"/>
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105 <param name="ref_file" value="hg38"/>
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106 <output name="output_table" file="test2-nobed.output" lines_diff="4"/>
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107 </test>
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108 </tests>
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109
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110 <help>
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111 <![CDATA[
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112
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113 **What it does**
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114
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115 This tool counts the number/proportion of mismatches per position along the read,
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116 for each read (see figure below).
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117
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118 .. image:: ${static_path}/images/snapshot_good.jpg
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119 :height: 350
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120 :width: 650
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121
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122 -----
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123
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124 **What is special**
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125
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126 By providing a bed file, tasmanian-mismatch will count mismatches from all regions depicted in the figure below,
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127 and will report them separately. Also, a parameter defined as *"confidence"* allows including reads with >=
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128 bases in the boundary region in a separate group. This is useful when the bed refers to repeat regions. Since these
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129 regions might not have been correctly placed in the assembly or are not the same in different individuals, we can
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130 include this *confidence* repeat regions where we have high confidence on the reference genome to which we mapped the reads.
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131
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132 .. image:: ${static_path}/images/intersections_tasmanian.jpg
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133 :height: 150
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134 :width: 650
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135
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136 Softclips are critical in FFPE (Formalin-fixed paraffin-embedded) experiments as mismatches tend to accumulate at the ends of the reads. Most often, softclips
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137 are all accepted during the analysis and many real mismatches are indirectly excluded from the analysis. Hence, this tool
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138 provides different ways to deal with this:
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139
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140 The *softclips* field allows for 3 different ways at treating softclips:
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141 0) Exclude these region if there is less than 2/3 identity with the reference genome
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142 1) Exclude all softclipped bases
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143 2) Include all softclipped bases
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144
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145 .. class:: warningmark
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146
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147 BAM/SAM file must be **sorted** if not using a bed file.
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148
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149 ]]>
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150 </help>
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151 <citations>
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152 <citation type="bibtex">
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153 @misc{githubtasmanian,
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154 author = {Langhorst B., Others, Erijman A.},
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155 year = {2020},
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156 title = {TBD},
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157 publisher = {GitHub},
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158 journal = {GitHub repository},
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159 url = {https://github.com/nebiolabs/tasmanian-mismatch},
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160 }
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161 </citation>
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162 </citations>
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163 </tool>