Mercurial > repos > iuc > data_manager_primer_scheme_bedfiles
annotate data_manager/install_primer_scheme_bedfiles.xml @ 2:b3710e492ee4 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
author | iuc |
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date | Mon, 22 Jun 2020 18:26:10 -0400 |
parents | cce5d9327cd6 |
children | a2953ef09fe1 |
rev | line source |
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2
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
iuc
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1 <tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.11" tool_type="manage_data" profile="19.05"> |
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ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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2 <requirements> |
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b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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3 <requirement type="package" version="2.24.0">requests</requirement> |
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ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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4 </requirements> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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5 <!-- fetch all the primers in one go --> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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6 <command detect_errors="exit_code"> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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7 python '$__tool_directory__/install_primer_scheme_bedfiles.py' |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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8 '${output_file}' |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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9 #if $input.input_type == "ARTIC" |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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10 --artic_primers '${input.primers}' |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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11 #else |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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12 --primer_file '${input.primer_input}' |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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13 --primer_name '${input.primer_name}' |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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14 --primer_description '${input.primer_description}' |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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15 #end if |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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16 </command> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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17 <inputs> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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18 <conditional name="input"> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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19 <param name="input_type" label="Choose the source for primer schemes" type="select"> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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20 <option value="ARTIC" selected="true">ARTIC SARS-CoV-2 Github page</option> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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21 <option value="history">History</option> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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22 </param> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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23 <when value="ARTIC"> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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24 <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch"> |
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cce5d9327cd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6"
iuc
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25 <option value="SARS-CoV-2-ARTICv1" selected="true">SARS-CoV-2 ARTIC v1</option> |
cce5d9327cd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6"
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26 <option value="SARS-CoV-2-ARTICv2" selected="true">SARS-CoV-2 ARTIC v2</option> |
cce5d9327cd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6"
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27 <option value="SARS-CoV-2-ARTICv3" selected="true">SARS-CoV-2 ARTIC v3</option> |
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ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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28 </param> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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29 </when> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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30 <when value="history"> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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31 <param name="primer_input" label="Select history item" type="data" format="bed" /> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
iuc
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32 <param name="primer_name" label="Name for this primer scheme" type="text" |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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33 help="Non-word characters will be removed from primer scheme name and spaces replaced with underscore (_)" /> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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34 <param name="primer_description" label="Description for primer scheme" type="text" /> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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35 </when> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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36 </conditional> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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37 </inputs> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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38 <outputs> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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39 <data name="output_file" format="data_manager_json"/> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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40 </outputs> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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41 <tests> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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42 <test> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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43 <param name="input_type" value="ARTIC" /> |
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cce5d9327cd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6"
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44 <param name="primers" value="SARS-CoV-2-ARTICv1,SARS-CoV-2-ARTICv2,SARS-CoV-2-ARTICv3"/> |
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ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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45 <output name="output_file"> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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46 <assert_contents> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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47 <has_text text="ARTIC"/> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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48 </assert_contents> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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49 </output> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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50 </test> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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51 <test> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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52 <param name="input_type" value="history" /> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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53 <param name="primer_input" ftype="bed" value="sample1.bed" /> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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54 <param name="primer_name" value="sample_primer" /> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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55 <param name="primer_description" value="sample primer scheme" /> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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56 <output name="output_file"> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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57 <assert_contents> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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58 <has_text text="sample_primer"/> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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59 </assert_contents> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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60 </output> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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61 </test> |
ae730ecdc7e7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit f78536f45aa5ce801251a9725e468a47de1be44a"
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62 </tests> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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63 <help><![CDATA[ |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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64 Amplicon sequencing for viral pathogens using the `PrimalSeq and iVar`_ relies on |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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65 identifying primer locations in a reference sequence using BED format files. This |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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66 data manager populates a Galaxy tool data table, either from files provided via |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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67 a history or via the ARTIC_ network Github repository. |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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68 |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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69 .. _PrimalSeq and iVar: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7 |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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70 .. _ARTIC: https://artic.network/ |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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71 ]]></help> |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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72 <citations> |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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73 <citation type="doi">10.1186/s13059-018-1618-7</citation> |
b3710e492ee4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 61b727022bd1b24a8843830a9c5f34ef66835694"
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parents:
1
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|
74 </citations> |
1
cce5d9327cd6
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6"
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0
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75 </tool> |