annotate temp.xml @ 14:bc39ae53be03 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit bcb1f256bca5591aa3df390a302c19d52fba14c2
author portiahollyoak
date Mon, 23 May 2016 06:53:10 -0400
parents 72156de89c7a
children 65ae84fc6689
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1 <tool id ="run_TEMP" name="TEMP" version=" 0.1.5">
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2 <description></description>
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3 <requirements>
10
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4 <!-- The following are classical toolshed packages and should be removed
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5 once conda is deemed stable-->
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6 <requirement type="package" version="1.6.922">bioperl</requirement>
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7 <requirement type="package" version="0.7.12">bwa</requirement>
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8 <requirement type="package" version="2.24">bedtools</requirement>
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9 <!-- end of toolshed package definitions -->
0
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10 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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11 <requirement type="package" version="0.7.13">bwa</requirement>
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12 <requirement type="package" version="2.25.0">bedtools</requirement>
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13 <requirement type="package" version="324">ucsc-twobittofa</requirement>
10
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14 <requirement type="package" version="0.1.19">samtools</requirement>
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15 </requirements>
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16 <stdio>
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17 <exit_code range="1:" />
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18 </stdio>
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19 <command><![CDATA[
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20 ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai &&
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21 ln -f -s "$alignment" alignment.sorted.bam &&
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22 bash $__tool_directory__/scripts/TEMP_Insertion.sh -x "$minimum_score_difference" -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$te_locations" -m "$mismatches" -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} &&
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23 bash $__tool_directory__/scripts/TEMP_Absence.sh -x "$minimum_score_difference" -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
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24 zip archive.zip *insertion* *excision* *absence* && mv archive.zip $archive &&
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25 mv alignment.insertion.refined.bp.summary $insertion_summary &&
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26 mv alignment.absence.refined.bp.summary $absence_summary
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27 ]]></command>
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28 <inputs>
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29 <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
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30 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
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31 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>
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32 <param format="bed" name="te_locations" type="data" label="TE Locations bed file"/>
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33 <param format="txt" name="median_insertsize" type="data" label="Median Insert Length"/>
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34 <param name="mismatches" min="0" max="5" type="integer" value="3" label="Allow this many mismatches when aligning to TEs"/>
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35 <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum score difference between optimal and suboptimal alignment to consider read uniquely mapped"></param>
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36 </inputs>
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37 <outputs>
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38 <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertion summary file" />
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39 <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absence summary file" />
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40 <data format="zip" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" />
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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="chr2l_bwa_mem.bam" ftype="bam"/>
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45 <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/>
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46 <param name="consensus_te_seqs" value="test_consensus.fa" ftype="fasta"/>
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47 <param name="te_locations" value="test_TE_annotation.gff3" ftype="bed"/>
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48 <param name="median_insertsize" value="median_insert_size" ftype="txt"/>
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49 <output name="insertion_summary" file="test_chromosome.insertion.refined.bp.summary" ftype="bed"/>
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50 <output name="absence_summary" file="test_chromosome.absence.refined.bp.summary" ftype="bed"/>
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51 </test>
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52 </tests>
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53 <help> <![CDATA[
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54
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55
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56 TEMP is a software package for detecting transposable elements (TEs) insertions and absences from pooled high-throughput sequencing data
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57
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58 Current version v1.04
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59
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60 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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61
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62 For TE insertion analysis run TEMP_Insertion.sh in script.
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63 For TE absence analysis run TEMP_Absence.sh in script.
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64
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65 Output files
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66 -------------
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67
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68
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69 For TE insertion analysis there are 14 columns in the summary file::
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70
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71 Column 1: The chromosome where the detected insertion happens.
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72 Column 2: The coordinate of the start position of the detected insertion.
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73 Column 3: The coordinate of the end position of the detected insertion.
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74 Column 4: The TE family that the detected insertion belongs to.
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75 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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76 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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77 Column 7: The total number of read pairs that support the detected insertion.
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78 Column 8: The estimated population frequency of the detected insertion.
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79 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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80 Columns 11 & 12: Same as Columns 9 & 10 except for the junction on the other strand.
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81 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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82 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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83
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84
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85 For TE absence analysis there are 9 columns in the summary file::
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86
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87 Column 1: The chromosome where the detected absence happens.
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88 Column 2: The coordinate of the start position of the detected absence.
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89 Column 3: The coordinate of the end position of the detected absence.
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90 Column 4: The TE family that the detected insertion belongs to.
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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91 Column 5: Junctions at 5’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands.
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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92 Column 6: Junctions at 3’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands.
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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93 Column 7: The number of reads supporting the absence.
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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94 Column 8: The number of reads supporting the reference (no absence).
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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95 Column 9: Estimated population frequency of the detected absence event.
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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96
0
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97
28d1a6f8143f planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
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98 ]]> </help>
12
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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99 <citations>
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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100 <citation type="doi">10.1093/nar/gku323</citation>
ca36262102d8 planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50
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101 </citations>
10
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102 </tool>