Mercurial > repos > iuc > biotradis

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

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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
children
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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_gene_insert_sites" name="Bio-TraDis counts to gene insertion data" version="@TOOL_VERSION@+galaxy@VERSION@">
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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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2 <description></description>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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3 <macros>
738e58ed9cc2 "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>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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5 </macros>
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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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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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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 tradis_gene_insert_sites -trim3 '$trim3' -trim5 '$trim5' '$input_annot' '$input_counts'
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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11 ]]>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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12 </command>
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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14 <inputs>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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15 <param name="input_counts" type="data" format="tabular" label="Read counts" help="Read counts at each nucleotide position for both strands. The first column contains forward strand counts, and the second contains reverse strand counts."/>
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16 <param name="input_annot" type="data" format="embl" label="EMBL file containing the reference genome annotations"/>
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17 <param name="trim3" type="float" value="0.1" min="0" max="1" label="Portion of the gene to trim in 3' end'" help="Trim reads at the 3'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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18 <param name="trim5" type="float" value="0" min="0" max="1" label="Portion of the gene to trim" help="Trim reads at the 5'end of genes. Some transposon insertions can be little disruptive when they occur end of genes. Trim to ignore these reads."/>
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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20 </inputs>
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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22 <outputs>
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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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23 <data name="gene_insert_sites" format="csv" from_work_dir="./*.csv" label="${tool.name} on ${on_string}"/>
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24 </outputs>
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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26 <tests>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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27 <test>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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28 <param name="input_counts" ftype="tabular" value="tiny.out.gz.CP009273.1_60_120.insert_site_plot.gz"/>
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29 <param name="input_annot" ftype="embl" value="tiny_ref.embl"/>
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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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30 <param name="trim3" ftype="float" value="0"/>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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31 <param name="trim5" ftype="float" value="0"/>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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32 <output name="gene_insert_sites" file="tiny.out.gz.CP009273.1_60_120.tradis_gene_insert_sites.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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33 </test>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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34 </tests>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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35 <help>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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36 <![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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38 **What is does**
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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40 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.
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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42 tradis_gene_insert_sites that combine the counts at each position and an annotation file to provide the number of reads and insertion for each feature.
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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44 -----
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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46 **Output files**
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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48 The tool outputs a table containing the columns :
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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49 - locus_tag
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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50 - gene_name
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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51 - ncrna : Is the feature a non-coding DNA. 1=yes, 0=no.
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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52 - start
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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53 - end
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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54 - strand
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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55 - read_count : Numer of reads mapping on the feature
738e58ed9cc2 "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
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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57 - gene_length
738e58ed9cc2 "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.
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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59 - fcn : Function
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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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61 -----
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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63 **More information**
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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65 .. 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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67 Additional information about Bio-TraDis can be found at https://github.com/sanger-pathogens/Bio-Tradis
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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68 ]]>
738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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69 </help>
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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71 <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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73 </tool>
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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738e58ed9cc2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/biotradis commit 1c0a0f88149bf8863a89c58bace81e070b3adb5a"
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