Mercurial > repos > mvdbeek > bam_readtagger

annotate findcluster.xml @ 48:54aafdb84833 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 45d0337e2a0d35e9a83d9c87c005c876c45ee054
author mvdbeek
date Wed, 12 Jun 2019 14:23:18 -0400
parents 21acaf15af89
children 534d6b4aebb0
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48
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1 <tool id="findcluster" name="Find clusters of reads" version="0.5.0">
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2 <description>in bam files</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <requirements>
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7 <requirement type="package" version="0.5.0">readtagger</requirement>
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8 </requirements>
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9 <version_command>findcluster --version</version_command>
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10 <command detect_errors="aggressive"><![CDATA[
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11 #import re
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12 #set sample_name = re.sub('[^\w\-_\.\,]', '_', str( $input.element_identifier))
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13 ln -f -s $input input.bam &&
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14 ln -f -s $input.metadata.bam_index input.bam.bai &&
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15 findcluster
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16 --input_path input.bam
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17 #if $transposon_source.ref_file:
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18 #if str($transposon_source.reference_source_selector) == "history":
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19 --transposon_reference_fasta '$transposon_source.ref_file'
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20 #else :
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21 --transposon_bwa_index '$transposon_source.ref_file.fields.path'
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22 #end if
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23 #end if
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24 #if $genome_source.ref_file:
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25 #if str($genome_source.reference_source_selector) == "history":
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26 --genome_reference_fasta '$genome_source.ref_file'
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27 #else :
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28 --genome_bwa_index '$genome_source.ref_file.fields.path'
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29 #end if
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30 #end if
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31 #if str($make_bam) == 'True':
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32 --output_bam '$output_bam'
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33 #end if
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34 #if str($make_vcf) == 'True'
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35 --output_vcf '$output_vcf'
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36 #end if
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37 #if str($make_gff) == 'True'
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38 --output_gff '$output_gff'
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39 #end if
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40 #if str($make_fasta) == 'True'
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41 --output_fasta '$output_fasta'
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42 #end if
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43 --sample_name '$sample_name'
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44 --threads "\${GALAXY_SLOTS:-2}"
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45 ]]></command>
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46 <inputs>
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47 <param name="input" argument="--input_path" type="data" format="bam"/>
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48 <param name="make_bam" type="boolean" truevalue="True" checked="true" label="Produce an alignment file containing evidence for insertions."/>
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49 <param name="make_vcf" type="boolean" truevalue="True" checked="true" label="Produce a VCF file describing the insertion that have been found."/>
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50 <param name="make_gff" type="boolean" truevalue="True" checked="false" label="produce a GFF file describing the insertions that have been found."/>
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51 <param name="make_fasta" type="boolean" checked="True" truevalue="True" label="Produce a fasta file containing assembled contigs."/>
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52 <expand macro="reference_source_conditional" reference_type="transposon"/>
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53 <expand macro="reference_source_conditional" reference_type="genome"/>
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54 </inputs>
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55 <outputs>
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56 <data name="output_bam" format="bam" label="findcluster BAM on $on_string">
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57 <filter>make_bam</filter>
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58 </data>
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59 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string">
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60 <filter>make_fasta</filter>
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61 </data>
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62 <data name="output_vcf" format="vcf" label="findcluster VCF on $on_string">
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63 <filter>make_vcf</filter>
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64 </data>
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65 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string">
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66 <filter>make_gff</filter>
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67 </data>
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68 </outputs>
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69 <tests>
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70 <test>
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71 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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72 <param name="make_gff" value="true"/>
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73 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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74 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" compare="sim_size"/>
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75 <output name="output_vcf" file="three_cluster_out.vcf" ftype="vcf" compare="sim_size"/>
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76 </test>
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77 <test>
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78 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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79 <param name="transposon_source|reference_source_selector" value="history"/>
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80 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/>
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81 <param name="make_gff" value="true"/>
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82 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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83 <output name="output_gff">
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84 <assert_contents>
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85 <has_text text="FBti0019066_rover_Gypsy" />
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86 </assert_contents>
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87 </output>
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88 </test>
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89 </tests>
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90 <help><![CDATA[
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91 .. code-block::
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92
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93 Usage: findcluster [OPTIONS]
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94
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95 Find clusters of reads that support a TE insertion.
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96
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97 Options:
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98 --input_path PATH Find cluster in this BAM file.
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99 --region TEXT Find clusters in this Region (Format is
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100 chrX:2000-1000).
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101 --max_proper_pair_size INTEGER Maximum proper pairs size. If not given will
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102 be inferred from the data.
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103 --output_bam PATH Write out BAM file with cluster information
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104 to this path. Reads will have an additional
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105 "CD" tag to indicate the cluster number
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106 --output_gff PATH Write out GFF file with cluster information
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107 to this path.
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108 --output_fasta PATH Write out supporting evidence for clusters
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109 to this path.
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110 --sample_name TEXT Sample name to use when writing out clusters
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111 in GFF file. Default is to infer the name
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112 from the input filename.
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113 --include_duplicates / --no-include_duplicates
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114 Include reads marked as duplicates when
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115 finding clusters.
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116 --transposon_reference_fasta TEXT
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117 Transposon fasta to align clipped reads to.
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118 Not necessary if BWA index is provided.
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119 --transposon_bwa_index TEXT Transposon BWA index to align clipped reads
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120 to
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121 --genome_reference_fasta TEXT Genome fasta to align clipped reads to. Not
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122 necessary if BWA index is provided.
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123 --genome_bwa_index TEXT Genome BWA index to align clipped reads to
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124 --threads INTEGER RANGE Threads to use for cap3 assembly step
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125 --shm_dir PATH Path to shared memory folder
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126 --version Show the version and exit.
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127 --help Show this message and exit.
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128
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129
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130 ]]></help>
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131 </tool>