Mercurial > repos > mvdbeek > bam_readtagger
annotate findcluster.xml @ 33:c7f140920cc1 draft
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8a8cc2ebb37a86df6a63be57acf86c9c299ac5bf-dirty
author | mvdbeek |
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date | Thu, 09 Nov 2017 06:49:15 -0500 |
parents | bf3d04937095 |
children | 240c901dedc0 |
rev | line source |
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33
c7f140920cc1
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8a8cc2ebb37a86df6a63be57acf86c9c299ac5bf-dirty
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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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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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4 <import>macros.xml</import> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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5 </macros> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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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> |
7625c594bc37
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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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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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit f28b0130760f515502b7858bd92adf948a942f39-dirty
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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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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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13 findcluster |
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14 --input_path input.bam |
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15 #if $transposon_source.ref_file: |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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16 #if str($transposon_source.reference_source_selector) == "history": |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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17 --transposon_reference_fasta '$transposon_source.ref_file' |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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18 #else : |
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c7f140920cc1
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 8a8cc2ebb37a86df6a63be57acf86c9c299ac5bf-dirty
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19 --transposon_bwa_index '$reference_source.ref_file.fields.path' |
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20 #end if |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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21 #end if |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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22 #if $genome_source.ref_file: |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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23 #if str($genome_source.reference_source_selector) == "history": |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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24 --genome_reference_fasta '$genome_source.ref_file' |
301316cb596a
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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25 #else : |
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26 --genome_bwa_index '$reference_source.ref_file.fields.path' |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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27 #end if |
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28 #end if |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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29 --output_bam '$output_bam' |
7625c594bc37
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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30 --output_gff '$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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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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34 ]]></command> |
7625c594bc37
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
mvdbeek
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35 <inputs> |
7625c594bc37
planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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36 <param name="input" argument="--input_path" type="data" format="bam"/> |
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37 |
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38 <expand macro="reference_source_conditional" reference_type="transposon"/> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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39 <expand macro="reference_source_conditional" reference_type="genome"/> |
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40 </inputs> |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 14a5033994a789097d1c61d1f3318397813d3d29-dirty
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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. |
31
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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82 --output_fasta PATH Write out supporting evidence for clusters |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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83 to this path. |
11
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
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84 --sample_name TEXT Sample name to use when writing out clusters |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
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85 in GFF file. Default is to infer the name |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
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86 from the input filename. |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
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87 --include_duplicates / --no-include_duplicates |
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88 Include reads marked as duplicates when |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 13fe863ca4079d83d897fdf7e394a7474eea6117-dirty
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89 finding clusters. |
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90 --transposon_reference_fasta TEXT |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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91 Transposon fasta to align clipped reads to. |
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92 Not necessary if BWA index is provided. |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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93 --transposon_bwa_index TEXT Transposon BWA index to align clipped reads |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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94 to |
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95 --genome_reference_fasta TEXT Genome fasta to align clipped reads to. Not |
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planemo upload for repository https://github.com/bardin-lab/readtagger/tree/master/galaxy commit 6e01a2e472ebbb07ce5181b836bae8bc5c7ecf36-dirty
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96 necessary if BWA index is provided. |
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97 --genome_bwa_index TEXT Genome BWA index to align clipped reads to |
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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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100 --version Show the version and exit. |
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101 --help Show this message and exit. |
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102 |
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103 |
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104 ]]></help> |
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105 </tool> |