annotate tradis_essentiality.xml @ 5:8e4a4f240961 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 5aac8c4c9990e8796c8a4c55d6c900c03e6db3c0
author iuc
date Wed, 13 Mar 2024 14:56:52 +0000
parents 103bd59b3e33
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58234d95978d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 61c83ac999a040604915ff7cf92670b2635b967e"
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1 <tool id="tradis_essentiality" name="Bio-TraDis Essentiality Predictions" version="@TOOL_VERSION@+galaxy@VERSION@">
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2 <description></description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
5
8e4a4f240961 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 5aac8c4c9990e8796c8a4c55d6c900c03e6db3c0
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6 <expand macro="xrefs"/>
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7 <expand macro="requirements" />
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8 <command detect_errors="aggressive">
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9 <![CDATA[
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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10 ln -s '$input_insert_file' input.csv &&
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11 tradis_essentiality.R input.csv
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12 ]]>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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13 </command>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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14 <inputs>
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15 <param name="input_insert_file" type="data" format="csv" label="Gene insertion counts" help="Ourput file of `Bio-TraDis counts to gene insertion data` tool"/>
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16 </inputs>
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17 <outputs>
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18 <data name="ess_genes" format="csv" label="${tool.name} on ${on_string}: Essential genes" from_work_dir="input.csv.essen.csv"/>
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19 <data name="ambig_genes" format="csv" label="${tool.name} on ${on_string}: Unclassified genes" from_work_dir="input.csv.ambig.csv"/>
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20 <data name="all_genes" format="csv" label="${tool.name} on ${on_string}: All genes" from_work_dir="input.csv.all.csv"/>
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21 <data name="qc_results" format="pdf" label="${tool.name} on ${on_string}: QC report" from_work_dir="input.csv.QC_and_changepoint_plots.pdf"/>
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22 </outputs>
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23 <tests>
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24 <test>
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25 <param name="input_insert_file" ftype="csv" value="test.csv"/>
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26 <output name="ess_genes" file="test.csv.essen.csv" compare="sim_size" delta="200" />
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27 <output name="ambig_genes" file="test.csv.ambig.csv" compare="sim_size" delta="200" />
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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28 <output name="all_genes" file="test.csv.all.csv" compare="sim_size" delta="200" />
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29 </test>
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30 </tests>
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31 <help>
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32 <![CDATA[
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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34 **What is does**
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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36 Bio-TraDis provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format.
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38 tradis_essentiality tool performs an Essentiality analysis using the annotation counts output of tradis_gene_insert_sites tool
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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40 -----
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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42 **Output files**
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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44 - Essential genes table : Table containing the essential genes
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45 - Unclassified genes : Table containing genes that couldn't be classified as essential or non essential
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46 - All genes : Table containing all genes
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47 - QC report : PDF file containing the regression plot
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48
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49 All tables contain the following columns:
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50 - locus_tag
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51 - gene_name
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52 - ncrna : Non-coding RNA, 1 if the feature is a non coding DNA, 0 if not.
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53 - start
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54 - end
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55 - strand
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56 - read_count : Total number of reads mapping on the feature
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57 - ins_index : Insertion index, number of insertion divided by the gene length
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58 - gene_length
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59 - ins_count : Number of insertion within the feature.
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60 - fcn : Function
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61
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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62 -----
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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64 **More information**
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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66 .. class:: infomark
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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68 Additional information about Bio-TraDis can be found at https://github.com/sanger-pathogens/Bio-Tradis
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69 ]]>
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70 </help>
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72 <expand macro="citations" />
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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74 </tool>
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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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