annotate temp.xml @ 5:2d566f713aec draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty
author portiahollyoak
date Mon, 25 Apr 2016 14:16:04 -0400
parents 8c8cc2e2c0bc
children 50c432ca4d1e
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1 <tool id ="run_TEMP" name="Run TEMP" version=" 0.1.0">
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2 <description></description>
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3 <requirements>
3
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4 <requirement type="package" version="0.1.19">samtools</requirement>
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5 <requirement type="package" version="1.6.924">perl-bioperl</requirement>
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6 <requirement type="package" version="0.7.13">bwa</requirement>
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7 <requirement type="package" version="2.25.0">bedtools</requirement>
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8 <requirement type="package" version="324">ucsc-twobittofa</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
5
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15 ln -f -s "$alignment.metadata.bam_index" "$alignment.element_identifier".sorted.bam.bai &&
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16 ln -f -s "$alignment" "$alignment.element_identifier".sorted.bam &&
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17 ls -l ;
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18 bash $__tool_directory__/scripts/TEMP_Insertion.sh -i "$alignment.element_identifier".sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && ls -l &&
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19 bash $__tool_directory__/scripts/TEMP_Absence.sh -i "$alignment.element_identifier".sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} &&
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20 mv "$alignment.element_identifier".insertion.bp.bed $insertion_bed &&
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21 mv "$alignment.element_identifier".insertion.refined.bp $insertion_bed_refined &&
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22 mv "$alignment.element_identifier".insertion.refined.bp.summary $insertion_summary &&
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23 mv "$alignment.element_identifier".absence.refined.bp.summary $absence_summary &&
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24 zip $archive *insertion* *excision* *absence*
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25 ]]></command>
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26 <inputs>
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27 <param format="bam" name="alignment" type="data" label="Alignment bam file"/>
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28 <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/>
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29 <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/>
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30 <param format="bed" name="bed_te_locations" type="data" label="TE Locations bed file"/>
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31 <!--
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32 <param format="tabular" name="te_families" type="data" label="TE Families"/>
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33 <param format="gff" name="gff_te_locations" type="data" label="Reference TE insertion Locations with Family ID names GFF file"/>
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34 -->
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35 <param format="txt" name="median_insertsize" type="data" label="Median Insert Length"/>
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36 </inputs>
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37 <outputs>
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38 <data format="bed" type="data" name="insertion_bed" Label="Insertion BED file" />
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39 <data format="bed" type="data" name="insertion_bed_refined" Label="Insertion BED file (refined)" />
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40 <data format="bed" type="data" name="insertion_summary" Label="Insertion summary file" />
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41 <data format="bed" type="data" name="absence_summary" Label="Absence summary file" />
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42 <data format="zip" type="data" name="archive" Label="Compressed output files" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="alignment" value="test_chromosome.sorted.bam" ftype="bam"/>
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47 <param name="reference2bit" value="dm3_chr2L.2bit" ftype="twobit"/>
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48 <param name="consensus_te_seqs" value="test_consensus.fa" ftype="fasta"/>
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49 <param name="bed_te_locations" value="test_TE_annotation.bed" ftype="bed"/>
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50 <output name="insertion_bed" file="test_chromosome.insertion.bp.bed" ftype="bed" />
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51 <output name="insertion_bed_refined" file="test_chromosome.insertion.refined.bp" ftype="bed"/>
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52 <output name="insertion_summary" file="test_chromosome.insertion.refined.bp.summary" ftype="bed"/>
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53 <output name="absence_summary" file="test_chromosome.absence.refined.bp.summary" ftype="bed"/>
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54 </test>
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55 </tests>
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56 <help> <![CDATA[
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57
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58
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59 TEMP is a software package for detecting transposable elements (TEs) insertions and absences from pooled high-throughput sequencing data
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60
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61 Current version v1.04
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62
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63 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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64
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65 For TE insertion analysis run TEMP_Insertion.sh in script.
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66 For TE absence analysis run TEMP_Absence.sh in script.
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67
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68
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69 ]]> </help>
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70 </tool>