Mercurial > repos > iuc > biotradis

annotate tradis_essentiality.xml @ 4:86c8fb3bb521 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 597c82a8fa756e68828ef201de7bb7e69d2c50bd
author iuc
date Mon, 04 Jul 2022 07:28:50 +0000
parents d1278922a88e
children
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e8cb43bd2fe4 "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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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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2 <description></description>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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3 <macros>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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4 <import>macros.xml</import>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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5 </macros>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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6 <expand macro="requirements" />
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d1278922a88e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 6a29aaead9d6b0f69ef70113df58047877fc6ce5"
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7 <command detect_errors="aggressive">
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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8 <![CDATA[
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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9 ln -s '$input_insert_file' input.csv &&
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d1278922a88e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 6a29aaead9d6b0f69ef70113df58047877fc6ce5"
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10 tradis_essentiality.R input.csv
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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11 ]]>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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12 </command>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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13 <inputs>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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14 <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"/>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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15 </inputs>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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16 <outputs>
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17 <data name="ess_genes" format="csv" label="${tool.name} on ${on_string}: Essential genes" from_work_dir="input.csv.essen.csv"/>
d1278922a88e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 6a29aaead9d6b0f69ef70113df58047877fc6ce5"
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18 <data name="ambig_genes" format="csv" label="${tool.name} on ${on_string}: Unclassified genes" from_work_dir="input.csv.ambig.csv"/>
d1278922a88e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 6a29aaead9d6b0f69ef70113df58047877fc6ce5"
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19 <data name="all_genes" format="csv" label="${tool.name} on ${on_string}: All genes" from_work_dir="input.csv.all.csv"/>
d1278922a88e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 6a29aaead9d6b0f69ef70113df58047877fc6ce5"
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20 <data name="qc_results" format="pdf" label="${tool.name} on ${on_string}: QC report" from_work_dir="input.csv.QC_and_changepoint_plots.pdf"/>
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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21 </outputs>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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22 <tests>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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23 <test>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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24 <param name="input_insert_file" ftype="csv" value="test.csv"/>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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25 <output name="ess_genes" file="test.csv.essen.csv" compare="sim_size" delta="200" />
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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26 <output name="ambig_genes" file="test.csv.ambig.csv" compare="sim_size" delta="200" />
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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27 <output name="all_genes" file="test.csv.all.csv" compare="sim_size" delta="200" />
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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28 </test>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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29 </tests>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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30 <help>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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31 <![CDATA[
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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33 **What is does**
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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35 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.
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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37 tradis_essentiality tool performs an Essentiality analysis using the annotation counts output of tradis_gene_insert_sites tool
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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39 -----
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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41 **Output files**
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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43 - Essential genes table : Table containing the essential genes
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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44 - Unclassified genes : Table containing genes that couldn't be classified as essential or non essential
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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45 - All genes : Table containing all genes
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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46 - QC report : PDF file containing the regression plot
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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48 All tables contain the following columns:
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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49 - locus_tag
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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50 - gene_name
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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51 - ncrna : Non-coding RNA, 1 if the feature is a non coding DNA, 0 if not.
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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52 - start
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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53 - end
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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54 - strand
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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55 - read_count : Total number of reads mapping on the feature
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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56 - ins_index : Insertion index, number of insertion divided by the gene length
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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57 - gene_length
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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58 - ins_count : Number of insertion within the feature.
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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59 - fcn : Function
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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61 -----
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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63 **More information**
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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65 .. class:: infomark
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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67 Additional information about Bio-TraDis can be found at https://github.com/sanger-pathogens/Bio-Tradis
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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68 ]]>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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69 </help>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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71 <expand macro="citations" />
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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73 </tool>
bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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bccf5ebe9b55 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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