Mercurial > repos > iuc > variant_analyzer
annotate mut2read.xml @ 0:8d29173d49a9 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
author | iuc |
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date | Wed, 20 Nov 2019 17:47:35 -0500 |
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children | 3556001ff2db |
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0
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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1 <?xml version="1.0" encoding="UTF-8"?> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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2 <tool id="mut2read" name="DCS mutations to tags/reads:" version="1.0.0" profile="19.01"> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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3 <description>Extracts all tags that carry a mutation in the duplex consensus sequence (DCS)</description> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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4 <macros> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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5 <import>va_macros.xml</import> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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6 </macros> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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7 <requirements> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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8 <requirement type="package" version="2.7">python</requirement> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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9 <requirement type="package" version="1.4.0">matplotlib</requirement> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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10 <requirement type="package" version="0.15">pysam</requirement> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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11 </requirements> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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12 <command><![CDATA[ |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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13 ln -s '$file2' bam_input.bam && |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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14 ln -s '${file2.metadata.bam_index}' bam_input.bam.bai && |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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15 python '$__tool_directory__/mut2read.py' |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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16 --mutFile '$file1' |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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17 --bamFile bam_input.bam |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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18 --familiesFile '$file3' |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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19 --outputFastq '$output_fastq' |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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20 --outputJson '$output_json' |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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21 ]]> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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22 </command> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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23 <inputs> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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24 <param name="file1" type="data" format="tabular" label="DCS Mutation File" optional="false" help="TABULAR file with DCS mutations. See Help section below for a detailed explanation."/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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25 <param name="file2" type="data" format="bam" label="DCS BAM File" optional="false" help="BAM file with aligned DCS reads."/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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26 <param name="file3" type="data" format="tabular" label="Aligned Families File" optional="false" help="TABULAR file with aligned families."/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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27 </inputs> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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28 <outputs> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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29 <data name="output_fastq" format="fastq" label="${tool.name} on ${on_string}: FASTQ"/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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30 <data name="output_json" format="json" label="${tool.name} on ${on_string}: JSON"/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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31 </outputs> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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32 <tests> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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33 <test> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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34 <param name="file1" value="DCS_Mutations_test_data_VA.tabular"/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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35 <param name="file2" value="DCS_test_data_VA.bam"/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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36 <param name="file3" value="Aligned_Families_test_data_VA.tabular"/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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37 <output name="output_fastq" file="Interesting_Reads_test_data_VA.fastq" lines_diff="136"/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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38 <output name="output_json" file="tag_count_dict_test_data_VA.json" lines_diff="2"/> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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39 </test> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
iuc
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40 </tests> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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41 <help> <![CDATA[ |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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42 **What it does** |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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43 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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44 Takes a tabular file with mutations, a BAM file of aligned DCS reads, and a |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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45 tabular file with aligned families as input and prints all tags of reads that |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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46 carry a mutation to a user specified output file and creates a fastq file of |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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47 reads of tags with a mutation. |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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48 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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49 **Input** |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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50 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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51 **Dataset 1:** Tabular file with duplex consesus sequence (DCS) mutations as |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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52 generated by the **Variant Annotator** tool. |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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53 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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54 **Dataset 2:** BAM file of aligned DCS reads. This file can be obtained by the |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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55 tool `Map with BWA-MEM <https://arxiv.org/abs/1303.3997>`_. |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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56 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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57 **Dataset 3:** Tabular file with reads as produced by the |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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58 **Du Novo: Align families** tool of the `Du Novo Analysis Pipeline |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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59 <https://doi.org/10.1186/s13059-016-1039-4>`_ |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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60 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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61 **Output** |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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62 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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63 The output is a json file containing dictonaries of the tags of reads containing mutations |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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64 in the DCS and a fastq file of all reads of these tags. |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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65 |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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66 ]]> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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67 </help> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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68 <expand macro="citation" /> |
8d29173d49a9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/variant_analyzer commit 5a438f76d0ecb6478f82dae6b9596bc7f5a4f4e8"
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69 </tool> |