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1 <?xml version="1.0"?>
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2 <tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1">
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3 <description/>
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4 <requirements><requirement type="package">mosaik</requirement></requirements>
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5 <command>
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6 #set $processors = '-p 4'
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7 #set $lm = ''
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8 #if $paired.kind == 'single':
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9 #set $mfl = ''
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10 #set $ls = ''
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11 #else:
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12 #set $ls = '-ls $mfl'
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13 #end if
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14 MosaikBuild -fr
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15 #if $genomeSource.refGenomeSource == 'indexed':
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16 ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] }
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17 #else:
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18 $genomeSource.historyReference
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19 #end if
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20 -oa mosaik_ref_file;
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21 MosaikBuild -q $reads $mfl -st $st -out mosaik_reads_file;
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22 MosaikAligner -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file $ls -mm $mm -mhp $mhp -act $act -bw $bw $processors $lm -hs 15;
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23 MosaikText -in mosaik_aligned_file -$outFormat sam_bam_file;
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24 #if str($outFormat) == 'bam':
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25 samtools sort sam_bam_file sorted_bam;
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26 mv sorted_bam.bam $output
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27 #else:
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28 gunzip sam_bam_file.gz;
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29 mv sam_bam_file $output
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30 #end if
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31 </command>
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32 <inputs>
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33 <conditional name="genomeSource">
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34 <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">
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35 <option value="indexed">Use a built-in index</option>
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36 <option value="history">Use one from the history</option>
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37 </param>
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38 <when value="indexed">
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39 <param name="indexReference" type="select" label="Select a reference genome">
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40 <options from_data_table="mosaik_indexes">
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41 <filter type="sort_by" column="2"/>
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42 <validator type="no_options" message="No indexes are available" />
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43 </options>
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44 </param>
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45 </when>
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46 <when value="history">
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47 <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/>
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48 </when>
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49 </conditional>
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50 <param format="fastq" name="reads" type="data" label="Fastq Reads File"/>
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51 <param name="outFormat" type="select" label="Output Format">
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52 <option value="sam">Sam</option>
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53 <option value="bam">Bam</option>
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54 </param>
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55 <param name="st" type="select" label="Sequencing Technology Used">
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56 <option value="454">454</option>
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57 <option value="illumina">Illumina</option>
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58 <option value="solid">Solid</option>
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59 <option value="sanger">Sanger</option>
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60 <option value="helicos">Helicos</option>
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61 </param>
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62 <conditional name="paired">
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63 <param name="kind" type="select" label="Is this library mate-paired?">
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64 <option value="single">Single-end</option>
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65 <option value="paired">Paired-end</option>
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66 </param>
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67 <when value="single"/>
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68 <when value="paired">
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69 <param name="mfl" type="integer" value="200" label="Insert Size" help="the length between the paired reads"/>
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70 <param name="ls" type="integer" value="50" label="Realignment Window" help="Window size to realign mate pairs that are out of position. Large values slow down performance"/>
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71 </when>
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72 </conditional>
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73 <param name="mm" size="5" type="integer" value="6" label="Mismatches allowed" help="mismatches allowed per sequence"/>
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74 <param name="act" size="5" type="integer" value="35" label="Alignment Candidate Threshold" help="determines which hash regions will be aligned with Smith Waterman"/>
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75 <param name="bw" size="5" type="integer" value="19" label="Smith-Waterman band width"/>
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76 <param name="mhp" size="5" type="integer" value="100" label="Maximum # Of Positions Stored Per Seed" help="number of places in the reference the aligner will try to place a particular hash"/>
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77 </inputs>
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78 <outputs>
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79 <data format="sam" name="output">
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80 <change_format>
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81 <when input="outFormat" value="bam" format="bam" />
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82 </change_format>
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83 <actions>
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84 <conditional name="genomeSource.refGenomeSource">
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85 <when value="indexed">
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86 <action type="metadata" name="dbkey">
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87 <option type="from_data_table" name="mosaik_indexes" column="1">
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88 <filter type="param_value" column="0" value="#" compare="startswith" keep="False" />
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89 <filter type="param_value" ref="genomeSource.indexReference" column="0" />
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90 </option>
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91 </action>
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92 </when>
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93 <when value="history">
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94 <action type="metadata" name="dbkey">
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95 <option type="from_param" name="genomeSource.historyReference" param_attribute="dbkey" />
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96 </action>
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97 </when>
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98 </conditional>
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99 </actions>
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100 </data>
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101 </outputs>
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102 <tests>
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103 <test>
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104 <param name="refGenomeSource" value="history"/>
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105 <param name="historyReference" ftype="fasta" value="mosaik_test_ref.fasta"/>
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106 <param name="reads" ftype="fastq" value="mosaik_test_input.fastq"/>
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107 <param name="outFormat" value="sam"/>
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108 <param name="st" value="454"/>
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109 <param name="kind" value="single"/>
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110 <param name="mm" value="6"/>
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111 <param name="act" value="35"/>
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112 <param name="bw" value="19"/>
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113 <param name="mhp" value="100"/>
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114 <output name="output" file="mosaik_test_out.sam" compare="sim_size" delta="0"/>
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115 </test>
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116 </tests>
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117 <help>
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118 This tool uses Mosaik to align reads to a reference sequence.
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119 </help>
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120 </tool>
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