Mercurial > repos > portiahollyoak > temp
annotate temp_insertions.xml @ 21:9672fe07a232 draft default tip
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
author | mvdbeek |
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date | Mon, 05 Dec 2016 09:58:47 -0500 |
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21
9672fe07a232
planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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1 <tool id ="TEMP_insertions" name="TEMP Insertion" version="0.3.0"> |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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2 <description>finds TE insertions relative to reference</description> |
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3 <requirements> |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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4 <requirement type="package" version="1.6.924=pl5.22.0_0">perl-bioperl</requirement> |
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5 <requirement type="package" version="0.7.13">bwa</requirement> |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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6 <requirement type="package" version="2.25.0">bedtools</requirement> |
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7 <requirement type="package" version="324">ucsc-twobittofa</requirement> |
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8 <requirement type="package" version="1.3.1">samtools</requirement> |
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9 </requirements> |
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10 <stdio> |
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11 <exit_code range="1:" /> |
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12 </stdio> |
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13 <command><![CDATA[ |
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14 ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && |
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15 ln -f -s "$alignment" alignment.sorted.bam && |
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16 bash $__tool_directory__/scripts/TEMP_Insertion.sh |
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17 -x "$minimum_score_difference" |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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18 -i alignment.sorted.bam |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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19 -s $__tool_directory__/scripts |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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20 -r "$consensus_te_seqs" |
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21 -t "$te_locations" |
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22 #if $te_families: |
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23 -u "$te_families" |
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24 #end if |
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25 -m "$mismatches" |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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26 -f "$median_insertsize" |
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27 -c \${GALAXY_SLOTS:-2} && |
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28 mv alignment.insertion.refined.bp.summary $insertion_summary |
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29 ]]></command> |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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30 <inputs> |
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31 <param format="bam" name="alignment" type="data" label="Alignment bam file"/> |
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32 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/> |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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33 <param format="bed" name="te_locations" type="data" label="TE Annotations bed file"/> |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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34 <param format="tabular" name="te_families" type="data" optional="True" label="TE Identifiers and Families"/> |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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35 <param name="median_insertsize" value="" type="integer" label="Median Insert Length"/> |
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36 <param name="mismatches" min="0" max="5" type="integer" value="3" label="Allow this many mismatches when aligning to TEs"/> |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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37 <param name="minimum_score_difference" type="integer" min="0" max="37" value="30" label="Minimum difference between mapping scores"/> |
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38 </inputs> |
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39 <outputs> |
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40 <data format="bed" name="insertion_summary" label="${alignment.element_identifier} Insertions" /> |
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41 </outputs> |
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42 <tests> |
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43 <test> |
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44 <param name="alignment" value="test_chromosome.sorted.bam" ftype="bam"/> |
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45 <param name="consensus_te_seqs" value="test_concensus.fa" ftype="fasta"/> |
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46 <param name="te_locations" value="test_TE_annotation.bed" ftype="bed"/> |
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47 <param name="median_insertsize" value="500" ftype="integer"/> |
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48 <param name="minimum_score_difference" value="0" ftype="integer"/> |
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49 <output name="insertion_summary" file="test_insertions_out.bed" ftype="bed" compare="sim_size"/> |
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50 </test> |
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51 </tests> |
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52 <help> <![CDATA[ |
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53 |
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54 |
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55 TEMP |
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56 ------------- |
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57 TEMP is a software package for detecting transposable elements (TEs) insertions and absences from pooled high-throughput sequencing data |
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58 |
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59 Current version v1.04 |
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60 |
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61 Author: Jiali Zhuang (jiali.zhuang@umassmed.edu) and Jie Wang (jie.wangj@umassmed.edu) Weng Lab, University of Massachusetts Medical School, Worcester, MA, USA |
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62 |
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63 *Input files/variables* |
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64 ------------------------- |
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65 * Alignment file in BAM format |
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66 * Reference genome used in aligning, in fasta or twobit format. |
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67 * Transposable Elements' Consensus Sequences in fasta format. |
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68 * Annotations of TEs in reference genome in bed format. |
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69 * TE Identifiers and Families (optional) - A file containing in the first column the TE names/identifiers from the consensus sequences file, and in the second column, their respective TE family names as in the TE annotations file. When supplied, if a detected insertion overlaps with an annotated TE of the same family, the detected insertion will be excluded from the results. |
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70 * Median Insert Length |
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71 * Number of Mismatches allowed (default 3) |
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72 * Minimum difference between mapping scores. The minimum difference in scores between the optimal and suboptimal alignments to consider a read uniquely mapped. |
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73 |
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74 *Output files* |
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75 ----------------- |
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76 * **In the Insertions output file there are 14 columns:** |
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77 * Column 1: The chromosome where the detected insertion happens. |
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78 * Column 2: The coordinate of the start position of the detected insertion. |
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79 * Column 3: The coordinate of the end position of the detected insertion. |
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80 * Column 4: The TE family that the detected insertion belongs to. |
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81 * Column 5: The direction of the insertion. “Plus” means that the TE is integrated with the plus strand of the genome while “minus” means the TE is integrated with the minus strand. |
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82 * Column 6: The class of the insertion. “1p1” means that the detected insertion is supported by reads at both sides. “2p” means the detected insertion is supported by more than 1 read at only 1 side. “Singleton” means the detected insertion is supported by only 1 read at 1 side. |
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83 * Column 7: The total number of read pairs that support the detected insertion. |
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84 * Column 8: The estimated population frequency of the detected insertion. |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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85 * Columns 9 & 10: The coordinate of a junction and the number of the reads supporting it. If the junction is not found column 9 will be the arithmetic mean of the start and end coordinates and column 10 will have the value 0. |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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86 * Columns 11 & 12: Same as Columns 9 & 10 except for the junction on the other strand. |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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87 * Column 13: The number of reads supporting the detected insertion at the 5’ end of the TE (not including junction spanning reads). |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
mvdbeek
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88 * Column 13: The number of reads supporting the detected insertion at the 3’ end of the TE (not including junction spanning reads). |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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89 |
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90 |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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91 ----- |
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92 |
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93 |
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94 * **In the Absences output file there are 14 columns:** |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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95 * Column 1: The chromosome where the detected absence happens. |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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96 * Column 2: The coordinate of the start position of the detected absence. |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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97 * Column 3: The coordinate of the end position of the detected absence. |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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98 * Column 4: The TE family that the detected insertion belongs to. |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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99 * Column 5: Junctions at 5’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands. |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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100 * Column 6: Junctions at 3’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands. |
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101 * Column 7: The number of reads supporting the absence. |
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102 * Column 8: The number of reads supporting the reference (no absence). |
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planemo upload for repository https://github.com/portiahollyoak/Tools commit 0fea84d05f8976b8360a8b4943ecb01b87e3ade0-dirty
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103 * Column 9: Estimated population frequency of the detected absence event. |
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104 |
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105 |
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106 ]]> </help> |
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107 <citations> |
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108 <citation type="doi">10.1093/nar/gku323</citation> |
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109 </citations> |
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110 </tool> |