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annotate mutationseq.xml @ 2:7de2cc3a24af draft default tip

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author morinlab
date Tue, 06 Dec 2016 20:03:54 -0500
parents 2864eb962e5a
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3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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1 <tool id="mutationseq" name="MutationSeq" version="4.3.6">
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2 <description>
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3 a feature based classifier for somatic mutation detection
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="4.3.6">mutationseq</requirement>
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7 <requirement type="package" version="4.3.6">mutationseq_python_environment</requirement>
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8 </requirements>
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9 <macros>
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10 <import>citations.xml</import>
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11 </macros>
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12 <command>
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13
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14 <!-- Linking BAM Indexs to current working directory -->
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15 #if $model_source.model_source_selector == "standard" or $model_source.model_source_selector == "solid" or $model_source.model_source_selector == "deepseq" or $model_source.model_source_selector == "titan_mode"
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16 ln -s $model_source.normal normal.bam;
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17 ln -s $model_source.normal.metadata.bam_index normal.bam.bai;
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18 ln -s $model_source.tumour tumour.bam;
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19 ln -s $model_source.tumour.metadata.bam_index tumour.bam.bai;
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20
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21 #else
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22 ln -s $model_source.input input.bam;
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23 ln -s $model_source.input.metadata.bam_index input.bam.bai;
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24
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25 #end if
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26
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27 <!-- Index Reference if from History -->
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28 #if $reference_source.reference_source_selector == "history":
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29 ln -s $reference_source.ref_file ref.fa;
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30 samtools faidx ref.fa;
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31 #end if
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32
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33 <!-- Run Mutation Seq -->
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34 #if $interval:
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35 for i in \$(cat $interval); do
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36 #end if
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37
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38 #if $model_source.model_source_selector == "titan_mode":
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39 \$MUTATIONSEQ_PYTHON_ENVIRONMENT_ROOT_DIR/bin/python2.7 \$MUTATIONSEQ_ROOT_DIR/preprocess.py
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40 #else:
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41 \$MUTATIONSEQ_PYTHON_ENVIRONMENT_ROOT_DIR/bin/python2.7 \$MUTATIONSEQ_ROOT_DIR/classify.py
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42 #end if
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43
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44 #if $reference_source.reference_source_selector == "history":
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45 reference:ref.fa
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46 #else:
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47 reference:${reference_source.ref_file.fields.path}
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48 #end if
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49
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50 #if $model_source.model_source_selector == "titan_mode":
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51 normal:normal.bam
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52 tumour:tumour.bam
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53 model:\$MUTATIONSEQ_ROOT_DIR/model_single_v4.0.2.npz
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54 --single
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55
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56 #elif $model_source.model_source_selector == "standard"
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57 normal:normal.bam
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58 tumour:tumour.bam
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59 model:\$MUTATIONSEQ_ROOT_DIR/model_v4.1.2.npz
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60
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61 #elif $model_source.model_source_selector == "standard_single"
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62 normal:input.bam
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63 model:\$MUTATIONSEQ_ROOT_DIR/model_single_v4.0.2.npz
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64 --single
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65
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66 #elif $model_source.model_source_selector == "solid"
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67 normal:normal.bam
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68 tumour:tumour.bam
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69 model:\$MUTATIONSEQ_ROOT_DIR/model_solid_v4.1.2.npz
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70
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71 #elif $model_source.model_source_selector == "deepseq"
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72 normal:normal.bam
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73 tumour:tumour.bam
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74 model:\$MUTATIONSEQ_ROOT_DIR/model_deep_v0.2.npz
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75 --deep
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76
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77 #elif $model_source.model_source_selector == "deepseq_single"
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78 normal:input.bam
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79 model:\$MUTATIONSEQ_ROOT_DIR/model_deep_single_v0.2.npz
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80 --single
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81 --deep
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82
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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83 #end if
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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84
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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85 #if $advancedsettings.filter.value == "all"
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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86 --all
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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87 #elif $advancedsettings.filter.value == "no_filter"
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88 --no_filter
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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89 #end if
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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90
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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91 #if $interval
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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92 -i \$i
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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93 #end if
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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94
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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95 #if $advancedsettings.positions:
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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96 -f $advancedsettings.positions
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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97 #end if
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98
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99 --threshold $advancedsettings.filter_prob
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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100
1
2864eb962e5a Uploaded
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101 | grep -v ".*no somatic mutation calls.*" >> ./output_noheader;
2
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102 echo "\##fileformat=VCFv4.2" > ./minimal_vcf_header;
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103 echo "#CHROM POS ID REF ALT QUAL FILTER INFO" >> ./minimal_vcf_header;
1
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104 cat ./minimal_vcf_header ./output_noheader > $output
0
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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105 #if $interval
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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106 ; done
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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107 #end if
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108 ;
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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109 </command>
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110 <inputs>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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111 <conditional name="reference_source">
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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112 <param label="Choose the source for the reference genome" name="reference_source_selector" type="select">
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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113 <option value="cached">Use a built-in genome</option>
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114 <option value="history">Use a genome from the history</option>
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115 </param>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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116 <when value="cached">
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117 <param label="Reference Genome File" name="ref_file" type="select">
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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118 <options from_data_table="fasta_indexes"/>
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119 </param>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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120 </when>
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121 <when value="history">
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122 <param label="Reference Genome File" name="ref_file" type="data" format="fasta"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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123 </when>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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124 </conditional>
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125 <conditional name="model_source">
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126 <param type="select" name="model_source_selector" label="Choose the model for MutationSeq">
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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127 <option value="standard" selected="true">Matched Sample Illumina Model</option>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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128 <option value="solid">Matched Sample Solid Model</option>
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129 <option value="deepseq">Matched Sample Deepseq Model</option>
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130 <option value="standard_single">Single Sample Illumina Model</option>
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131 <option value="deepseq_single">Single Sample Deepseq Model</option>
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132 <option value="titan_mode">TITAN Mode</option>
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133 </param>
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134 <when value="standard">
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135 <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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136 <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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137 </when>
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138 <when value="solid">
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139 <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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140 <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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141 </when>
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142 <when value="deepseq">
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143 <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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144 <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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145 </when>
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146 <when value="standard_single">
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147 <param type="data" format="bam" name="input" label="Sequence Alignment File"/>
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148 </when>
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149 <when value="deepseq_single">
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150 <param type="data" format="bam" name="input" label="Sequence Alignment File"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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151 </when>
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152 <when value="titan_mode">
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153 <param type="data" format="bam" name="normal" label="Normal Alignment File"/>
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154 <param type="data" format="bam" name="tumour" label="Tumour Alignment File"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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155 </when>
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156 </conditional>
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157 <param type="data" format="txt" optional="true" name="interval" label="Specify Interval"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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158 <section name="advancedsettings" title="Advanced Settings" expanded="false">
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159 <param type="select" name="filter" label="Filter Method">
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160 <option value="standard" selected="true">Print Probablistic Positions</option>
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161 <option value="all">Print Positions Regardless of Classified Probabilitly</option>
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162 <option value="no_filter">Print Positions Regardless of Initial Criteira</option>
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163 </param>
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164 <param type="data" format="txt" optional="true" name="positions" label="Positions File"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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165 <param type="float" value="0.85" min="0" max="1" name="filter_prob" label="Probabililty Filter Threshold"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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166 </section>
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167 </inputs>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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168 <outputs>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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169 <data format="vcf" name="output"/>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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170 </outputs>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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171 <citations>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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172 <expand macro="morinlab_citation" />
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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173 <expand macro="galaxy_citation" />
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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174 <expand macro="mutationseq_citation" />
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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175 </citations>
3f5545f5f0c8 planemo upload for repository https://github.com/morinlab/tools-morinlab/tree/master/tools/mutationseq commit 4ef2d91b7c1686a2696b92fe538d4aec51d05e40-dirty
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176 </tool>