Mercurial > repos > iuc > tasmanian_mismatch

annotate Tasmanian.xml @ 0:bc0b40dec7d2 draft

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"planemo upload for repository https://github.com/nebiolabs/tasmanian-mismatch commit a64a371ca1ed117c9bd8af743d847128fbce461c"
author iuc
date Wed, 20 May 2020 17:23:42 -0400
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children b15fbf90db53
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bc0b40dec7d2 "planemo upload for repository https://github.com/nebiolabs/tasmanian-mismatch commit a64a371ca1ed117c9bd8af743d847128fbce461c"
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1 <tool id="tasmanian_mismatch" name="Analysis of artifacts with Tasmanian" version="0.1.3" profile="18.09">
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2 <requirements>
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3 <requirement type="package" version="0.1.3">tasmanian-mismatch</requirement>
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4 <requirement type="package" version="1.9">samtools</requirement>
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5 </requirements>
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6 <command detect_errors="exit_code">
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7 <![CDATA[
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8
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9 #set $reference_fasta_filename = "localref.fa"
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10
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11 #if str( $reference_source.reference_source_selector ) == "history":
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12 ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
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13 #else:
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14 #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
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15 #end if
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17 samtools view '${bam_input}' |
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19 #if $bed_filename
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20 run_intersections -b '$bed_filename' |
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21 #end if
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23 run_tasmanian
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24 -q '${basequality}'
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25 -s '${softclips}'
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26 -m '${mapquality}'
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27 -c '${confidence}'
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28 -r '${reference_fasta_filename}' > '${output_table}'
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30 ]]></command>
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31 <inputs>
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32 <!-- Bam alignment file -->
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33 <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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34 <!-- reference genome upload -->
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35 <conditional name="reference_source">
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36 <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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37 <option value="cached">Local cache</option>
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38 <option value="history">History</option>
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39 </param>
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40 <when value="cached">
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41 <param name="ref_file" type="select" label="Select the reference genome from the list">
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42 <options from_data_table="all_fasta">
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43 <filter type="sort_by" column="2" />
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44 <validator type="no_options" message="No indexes are available" />
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45 </options>
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46 </param>
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47 </when>
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48 <when value="history">
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49 <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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50 </when>
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51 </conditional>
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52
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53 <!-- bed file -->
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54 <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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55
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56 <!-- Additional parameters -->
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57 <param name="confidence" label="Boundary" type="integer" value="20" min="0" max="100"
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58 help="Number of bases in boundary region, from 0 to length of the read (read help below). Default=20"/>
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59 <param name="softclips" label="Choose an action with softclips" type="select" display="radio"
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60 help="How sofclips whould be treated. Values include 0,1 or 2 (read the help below). Default=0">
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61 <option value="1">Never use softcliped bases</option>
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62 <option value="2">Always use softcliped bases</option>
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63 <option value="0" selected="True">Automatic desicion (Default)</option>
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64 </param>
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65 <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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66 <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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67 <param name="keepHTML_conditional" type="select" label="keep HTML output file?">
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68 <option value="yes">Yes</option>
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69 <option value="no">No</option>
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70 </param>
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71 </inputs>
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72
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73 <outputs>
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74 <data name="output_table" format="txt" />
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75 <data format="html" name="html_file" from_work_dir="Tasmanian_artifact_report.html" label="tasmanian-mismatch results table">
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76 <filter>keepHTML_conditional == "yes"</filter>
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77 </data>
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78 </outputs>
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79
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80 <tests>
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81 <!-- test when reference from history with bed-->
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82 <test>
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83 <param name="bam_input" value="test2.bam" ftype="bam"/>
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84 <param name="reference_source_selector" value="history"/>
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85 <param name="ref_file" value="small_region.fa"/>
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86 <param name="bed_filename" value="test2.bed" ftype="bed"/>
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87 <output name="output_table" file="test2-bed.output" lines_diff="4"/>
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88 </test>
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89 <!-- test when reference from history without bed-->
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90 <test>
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91 <param name="bam_input" value="test2.bam" ftype="bam"/>
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92 <param name="reference_source_selector" value="history"/>
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93 <param name="ref_file" value="small_region.fa"/>
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94 <output name="output_table" file="test2-nobed.output" lines_diff="4"/>
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95 </test>
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96 <!-- test when reference from cached-->
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97 <test>
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98 <param name="bam_input" value="test2.bam" ftype="bam" dbkey="hg38"/>
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99 <param name="reference_source_selector" value="cached"/>
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100 <param name="ref_file" value="hg38"/>
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101 <output name="output_table" file="test2-nobed.output" lines_diff="4"/>
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102 </test>
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103 </tests>
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104
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105 <help>
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106 <![CDATA[
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107
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108 **What it does**
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109
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110 This tool counts the number/proportion of mismatches per position along the read,
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111 for each read (see figure below).
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112
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113 .. image:: ${static_path}/images/snapshot_good.jpg
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114 :height: 350
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115 :width: 650
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116
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117 -----
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118
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119 **What is special**
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120
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121 By providing a bed file, tasmanian-mismatch will count mismatches from all regions depicted in the figure below,
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122 and will report them separately. Also, a parameter defined as *"confidence"* allows including reads with >=
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123 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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124 regions might not have been correctly placed in the assembly or are not the same in different individuals, we can
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125 include this *confidence* repeat regions where we have high confidence on the reference genome to which we mapped the reads.
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126
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127 .. image:: ${static_path}/images/intersections_tasmanian.jpg
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128 :height: 150
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129 :width: 650
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130
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131 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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132 are all accepted during the analysis and many real mismatches are indirectly excluded from the analysis. Hence, this tool
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133 provides different ways to deal with this:
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134
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135 The *softclips* field allows for 3 different ways at treating softclips:
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136 0) Exclude these region if there is less than 2/3 identity with the reference genome
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137 1) Exclude all softclipped bases
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138 2) Include all softclipped bases
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139
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140 .. class:: warningmark
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141
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142 BAM/SAM file must be **sorted** if not using a bed file.
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143
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144 ]]>
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145 </help>
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146 <citations>
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147 <citation type="bibtex">
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148 @misc{githubtasmanian,
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149 author = {Langhorst B., Others, Erijman A.},
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150 year = {2020},
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151 title = {TBD},
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152 publisher = {GitHub},
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153 journal = {GitHub repository},
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154 url = {https://github.com/nebiolabs/tasmanian-mismatch},
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155 }
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156 </citation>
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157 </citations>
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158 </tool>