annotate temp.xml @ 18:e198b686bfe4 draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit edf843bf10fa262f075980626a9201078f868757
author mvdbeek
date Wed, 17 Aug 2016 11:49:25 -0400
parents e7d3dc3e0ec9
children e541089245ba
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool id ="run_TEMP" name="TEMP" version="0.2.1">
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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 -->
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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 $__tool_directory__/scripts/TEMP_Insertion.sh
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23 -x "$minimum_score_difference"
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24 -i alignment.sorted.bam
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25 -s $__tool_directory__/scripts
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26 -r "$consensus_te_seqs"
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27 -t "$te_locations"
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28 #if $te_families:
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29 -u "$te_families"
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30 #end if
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31 -m "$mismatches"
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32 -f "$median_insertsize"
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33 -c \${GALAXY_SLOTS:-2} &&
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34 bash $__tool_directory__/scripts/TEMP_Absence.sh
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35 -x "$minimum_score_difference"
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36 -i alignment.sorted.bam
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37 -s $__tool_directory__/scripts
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38 -r "$te_locations"
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39 -t "$reference2bit"
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40 -f "$median_insertsize"
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41 -c \${GALAXY_SLOTS:-2} &&
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42 mv alignment.insertion.refined.bp.summary $insertion_summary &&
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43 mv alignment.absence.refined.bp.summary $absence_summary &&
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44 tar -czf archive.tar.gz *insertion* *excision* *absence* && mv archive.tar.gz $archive
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45 ]]></command>
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46 <inputs>
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47 <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
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48 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
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49 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>
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50 <param format="bed" name="te_locations" type="data" label="TE Annotations bed file"/>
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51 <param format="tabular" name="te_families" type="data" optional="True" label="TE Identifiers and Families"/>
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52 <param name="median_insertsize" value="" type="integer" label="Median Insert Length"/>
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53 <param name="mismatches" min="0" max="5" type="integer" value="3" label="Allow this many mismatches when aligning to TEs"/>
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54 <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum difference between mapping scores"/>
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55 </inputs>
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56 <outputs>
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57 <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertions" />
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58 <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absences" />
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59 <data format="tar" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" />
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/>
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64 <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/>
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65 <param name="consensus_te_seqs" value="test_consensus.fa" ftype="fasta"/>
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66 <param name="te_locations" value="test_TE_annotation.gff3" ftype="bed"/>
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67 <param name="median_insertsize" value="500" ftype="integer"/>
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68 <output name="insertion_summary" file="test_chromosome.insertion.refined.bp.summary" ftype="bed"/>
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69 <output name="absence_summary" file="test_chromosome.absence.refined.bp.summary" ftype="bed"/>
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70 </test>
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71 </tests>
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72 <help> <![CDATA[
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73
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74
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75 TEMP
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76 -------------
0
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77 TEMP is a software package for detecting transposable elements (TEs) insertions and absences from pooled high-throughput sequencing data
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78
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79 Current version v1.04
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80
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81 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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82
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83 *Input files/variables*
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84 -------------------------
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85 * Alignment file in BAM format
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86 * Reference genome used in aligning, in fasta or twobit format.
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87 * Transposable Elements' Consensus Sequences in fasta format.
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88 * Annotations of TEs in reference genome in bed format.
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89 * 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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90 * Median Insert Length
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91 * Number of Mismatches allowed (default 3)
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92 * 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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93
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94 *Output files*
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95 -----------------
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96 * **In the Insertions output file there are 14 columns:**
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97 * Column 1: The chromosome where the detected insertion happens.
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98 * Column 2: The coordinate of the start position of the detected insertion.
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99 * Column 3: The coordinate of the end position of the detected insertion.
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100 * Column 4: The TE family that the detected insertion belongs to.
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101 * 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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102 * 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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103 * Column 7: The total number of read pairs that support the detected insertion.
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104 * Column 8: The estimated population frequency of the detected insertion.
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105 * 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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106 * Columns 11 & 12: Same as Columns 9 & 10 except for the junction on the other strand.
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107 * 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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108 * 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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109
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110
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111 -----
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112
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113
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114 * **In the Absences output file there are 14 columns:**
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115 * Column 1: The chromosome where the detected absence happens.
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116 * Column 2: The coordinate of the start position of the detected absence.
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117 * Column 3: The coordinate of the end position of the detected absence.
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118 * Column 4: The TE family that the detected insertion belongs to.
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119 * 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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120 * 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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121 * Column 7: The number of reads supporting the absence.
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122 * Column 8: The number of reads supporting the reference (no absence).
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123 * Column 9: Estimated population frequency of the detected absence event.
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124
0
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125
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126 ]]> </help>
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127 <citations>
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128 <citation type="doi">10.1093/nar/gku323</citation>
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129 </citations>
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130 </tool>