Mercurial > repos > mvdbeek > bam_readtagger

annotate findcluster.xml @ 33:c7f140920cc1 draft

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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8a8cc2ebb37a86df6a63be57acf86c9c299ac5bf-dirty
author mvdbeek
date Thu, 09 Nov 2017 06:49:15 -0500
parents bf3d04937095
children 240c901dedc0
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33
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1 <tool id="findcluster" name="Find clusters of reads" version="0.4.0">
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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="0.4.0">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 ln -f -s $input input.bam &&
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12 ln -f -s $input.metadata.bam_index input.bam.bai &&
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13 findcluster
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14 --input_path input.bam
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15 #if $transposon_source.ref_file:
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16 #if str($transposon_source.reference_source_selector) == "history":
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17 --transposon_reference_fasta '$transposon_source.ref_file'
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18 #else :
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19 --transposon_bwa_index '$reference_source.ref_file.fields.path'
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20 #end if
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21 #end if
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22 #if $genome_source.ref_file:
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23 #if str($genome_source.reference_source_selector) == "history":
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24 --genome_reference_fasta '$genome_source.ref_file'
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25 #else :
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26 --genome_bwa_index '$reference_source.ref_file.fields.path'
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27 #end if
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28 #end if
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29 --output_bam '$output_bam'
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30 --output_gff '$output_gff'
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31 --output_fasta '$output_fasta'
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32 --sample_name '$input.element_identifier'
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33 --threads "\${GALAXY_SLOTS:-2}"
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34 ]]></command>
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35 <inputs>
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36 <param name="input" argument="--input_path" type="data" format="bam"/>
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38 <expand macro="reference_source_conditional" reference_type="transposon"/>
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39 <expand macro="reference_source_conditional" reference_type="genome"/>
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40 </inputs>
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41 <outputs>
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42 <data name="output_bam" format="bam" label="findcluster BAM on $on_string"/>
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43 <data name="output_fasta" format="fasta" label="findcluster contigs on $on_string"/>
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44 <data name="output_gff" format="gff3" label="findcluster GFF on $on_string"/>
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45 </outputs>
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46 <tests>
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47 <test>
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48 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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49 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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50 <output name="output_gff" file="three_cluster_out.gff" ftype="gff3" lines_diff="0"/>
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51 </test>
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52 <test>
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53 <param name="input" value="extended_and_annotated_roi.bam" ftype="bam"/>
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54 <param name="transposon_source|reference_source_selector" value="history"/>
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55 <param name="transposon_source|ref_file" value="reference.fasta" ftype="fasta"/>
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56 <output name="output_bam" file="three_cluster_out.bam" ftype="bam" lines_diff="2"/>
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57 <output name="output_gff">
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58 <assert_contents>
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59 <has_text text="FBti0019066_rover_Gypsy" />
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60 </assert_contents>
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61 </output>
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62 </test>
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63 </tests>
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64 <help><![CDATA[
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65 .. code-block::
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66
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67 Usage: findcluster [OPTIONS]
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68
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69 Find clusters of reads that support a TE insertion.
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70
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71 Options:
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72 --input_path PATH Find cluster in this BAM file.
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73 --region TEXT Find clusters in this Region (Format is
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74 chrX:2000-1000).
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75 --max_proper_pair_size INTEGER Maximum proper pairs size. If not given will
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76 be inferred from the data.
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77 --output_bam PATH Write out BAM file with cluster information
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78 to this path. Reads will have an additional
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79 "CD" tag to indicate the cluster number
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80 --output_gff PATH Write out GFF file with cluster information
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81 to this path.
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82 --output_fasta PATH Write out supporting evidence for clusters
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83 to this path.
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84 --sample_name TEXT Sample name to use when writing out clusters
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85 in GFF file. Default is to infer the name
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86 from the input filename.
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mvdbeek
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87 --include_duplicates / --no-include_duplicates
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88 Include reads marked as duplicates when
124f7f8ee080 planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
mvdbeek
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89 finding clusters.
31
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mvdbeek
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90 --transposon_reference_fasta TEXT
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mvdbeek
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91 Transposon fasta to align clipped reads to.
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mvdbeek
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92 Not necessary if BWA index is provided.
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mvdbeek
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93 --transposon_bwa_index TEXT Transposon BWA index to align clipped reads
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mvdbeek
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94 to
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mvdbeek
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95 --genome_reference_fasta TEXT Genome fasta to align clipped reads to. Not
301316cb596a planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
mvdbeek
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96 necessary if BWA index is provided.
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mvdbeek
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97 --genome_bwa_index TEXT Genome BWA index to align clipped reads to
11
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mvdbeek
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98 --threads INTEGER RANGE Threads to use for cap3 assembly step
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99 --shm_dir PATH Path to shared memory folder
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mvdbeek
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100 --version Show the version and exit.
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101 --help Show this message and exit.
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102
4
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103
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104 ]]></help>
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105 </tool>