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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit af32e767fd29667d3e29f1a202ad59d3dd498c84-dirty"
author jjohnson
date Mon, 30 Mar 2020 22:06:19 -0400
parents ba3910d7bd99
children
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ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
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1 <tool id="transindel" name="transIndel" version="@VERSION@.0" python_template_version="3.5">
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2 <description>detect indels from RNAseq or DNAseq BWA-MEM mapping</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
ba3910d7bd99 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/transindel commit f102f45fafcda3ee868765784d2f69d2dcad6233-dirty"
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6 <expand macro="requirements" />
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7 <expand macro="version_command" />
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8 <command detect_errors="exit_code"><![CDATA[
3
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9 ln -s -f '${analyze.input}' 'input.bam' &&
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10 ln -s -f '${analyze.input.metadata.bam_index}' 'input.bai' &&
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11 #if $analyze.input_src == 'RNA'
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12 #if $analyze.rfasta.rfasta_source == "history":
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13 ln -s '$analyze.rfasta.ref_fa_hist' ref.fa &&
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14 #else:
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15 ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa &&
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16 #end if
3
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17 transIndel_build_RNA.py -i 'input.bam' -o 'transIndel.bam'
0
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18 ## Get reference FASTA
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19 -r ref.fa
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20 ## Get reference GTF
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21 #if $analyze.rgtf.rgtf_source == "history":
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22 -g '$analyze.rgtf.ref_gtf_hist'
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23 #else:
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24 -g '$analyze.rgtf.ref_gtf_builtin.fields.path'
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25 #end if
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26 --mapq_cutoff $analyze.mapq_cutoff
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27 --max_del_length $analyze.max_del_length
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28 #if $analyze.transIndel_call.run_transIndel_call == 'yes'
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29 && transIndel_call.py -i 'transIndel.bam' -o transIndel
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30 -r ref.fa
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31 -c $analyze.transIndel_call.call_opts.min_observation_count
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32 -d $analyze.transIndel_call.call_opts.min_depth
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33 -f $analyze.transIndel_call.call_opts.min_allele_frequency
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34 -l $analyze.transIndel_call.call_opts.min_length
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35 -m $analyze.transIndel_call.call_opts.min_mapq
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36 #if $analyze.transIndel_call.call_opts.regions.regions_source != 'none':
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37 -t '$analyze.transIndel_call.call_opts.regions.target'
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38 #end if
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39 #end if
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40 #elif $analyze.input_src == 'DNA'
3
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41 transIndel_build_DNA.py -i 'input.bam' -o 'transIndel.bam'
0
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42 --mapq_cutoff $analyze.mapq_cutoff
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43 --max_del_length $analyze.max_del_length
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44 #if $analyze.transIndel_call.run_transIndel_call == 'yes'
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45 #if $analyze.rfasta.rfasta_source == "history":
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46 && ln -s '$analyze.transIndel_call.rfasta.ref_fa_hist' ref.fa
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47 #else:
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48 && ln -s '$analyze.transIndel_call.rfasta.ref_fa_builtin.fields.path' ref.fa
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49 #end if
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50 && transIndel_call.py -i 'transIndel.bam' -o transIndel
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51 -r ref.fa
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52 -c $analyze.transIndel_call.call_opts.min_observation_count
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53 -d $analyze.transIndel_call.call_opts.min_depth
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54 -f $analyze.transIndel_call.call_opts.min_allele_frequency
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55 -l $analyze.transIndel_call.call_opts.min_length
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56 -m $analyze.transIndel_call.call_opts.min_mapq
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57 #if $analyze.transIndel_call.call_opts.regions.regions_source != 'none':
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58 -t '$analyze.transIndel_call.call_opts.regions.target'
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59 #end if
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60 #end if
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61 #elif $analyze.input_src == 'transIndel'
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62 #if $analyze.rfasta.rfasta_source == "history":
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63 ln -s '$analyze.rfasta.ref_fa_hist' ref.fa &&
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64 #else:
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65 ln -s '$analyze.rfasta.ref_fa_builtin.fields.path' ref.fa &&
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66 #end if
3
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67 transIndel_call.py -i 'input.bam' -o 'transIndel'
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68 -r ref.fa
0
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69 -c $analyze.call_opts.min_observation_count
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70 -d $analyze.call_opts.min_depth
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71 -f $analyze.call_opts.min_allele_frequency
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72 -l $analyze.call_opts.min_length
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73 -m $analyze.call_opts.min_mapq
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74 #if $analyze.call_opts.regions.regions_source != 'none':
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75 -t '$analyze.call_opts.regions.target'
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76 #end if
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77 #end if
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78 ]]></command>
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79 <inputs>
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80 <conditional name="analyze">
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81 <param name="input_src" type="select" label="">
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82 <option value="RNA">RNA bwa-mem bam</option>
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83 <option value="DNA">DNA bwa-mem bam</option>
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84 <option value="transIndel">transIndel bam</option>
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85 </param>
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86 <when value="RNA">
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87 <param name="input" type="data" format="bam" label="bwa-mem bam from RNAseq data"/>
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88 <expand macro="reference_genome"/>
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89 <expand macro="reference_gtf"/>
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90 <param name="splice_site_half_bin_size" argument="-s" type="integer" value="20" min="0" label="splice site half bin size" help="(splice site half bin size)"/>
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91 <expand macro="build_opts" token_default_mapq_cutoff="60"/>
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92 <expand macro="transindel_call"/>
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93 </when>
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94 <when value="DNA">
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95 <param name="input" type="data" format="bam" label="bwa-mem bam from DNAseq data"/>
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96 <expand macro="build_opts" token_default_mapq_cutoff="15"/>
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97 <expand macro="transindel_call">
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98 <expand macro="reference_genome"/>
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99 </expand>
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100 </when>
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101 <when value="transIndel">
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102 <param name="input" type="data" format="bam" label="transIndel bam"/>
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103 <expand macro="reference_genome"/>
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104 <expand macro="call_opts"/>
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105 </when>
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106 </conditional>
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107 </inputs>
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108 <outputs>
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109 <data name="output_bam" format="bam" label="${tool.name} on ${on_string}: transIndel.bam" from_work_dir="transIndel.bam">
3
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110 <filter>analyze['input_src'] != 'transIndel'</filter>
0
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111 </data>
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112 <data name="output_vcf" format="vcf" label="${tool.name} on ${on_string}: transIndel.indel.vcf" from_work_dir="transIndel.indel.vcf" >
3
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113 <filter>analyze['input_src'] == 'transIndel' or analyze['transIndel_call']['run_transIndel_call'] == 'yes'</filter>
0
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114 </data>
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115 </outputs>
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116 <tests>
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117 <test>
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118 <conditional name="analyze">
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119 <param name="input_src" value="RNA"/>
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120 <param name="input" ftype="bam" value="RNA.bam"/>
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121 <conditional name="rfasta">
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122 <param name="rfasta_source" value="history"/>
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123 <param name="ref_fa_hist" ftype="fasta" value="GRCh38_20.fa" />
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124 </conditional>
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125 <conditional name="rgtf">
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126 <param name="rgtf_source" value="history"/>
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127 <param name="ref_gtf_hist" ftype="gtf" value="GRCh38_20.gtf" />
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128 </conditional>
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129 </conditional>
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130 <output name="output_vcf">
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131 <assert_contents>
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132 <has_text text="SVTYPE=DEL" />
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133 </assert_contents>
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134 </output>
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135 </test>
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136 </tests>
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137 <help><![CDATA[
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138 TODO: Fill in help.
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139 ]]></help>
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140 <expand macro="citations" />
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141 </tool>