Mercurial > repos > iuc > cooc_pubmut

annotate cooc_pubmut.xml @ 0:faaae22ddea8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
author iuc
date Thu, 11 Aug 2022 13:47:15 +0000
parents
children 06e4aed6a606
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0
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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1 <tool id="cooc_pubmut" name="Cojac: pubmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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2 profile="@PROFILE@">
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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3 <description>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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4 render a JSON or YAML file to a pretty table
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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5 </description>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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6 <macros>
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7 <import>macros.xml</import>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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8 </macros>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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9 <expand macro="biotools"/>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
iuc
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10 <expand macro="requirements">
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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11 <requirement type="package" version="2.12">pandoc</requirement>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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12 </expand>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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13 <expand macro="version"/>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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14 <command detect_errors="exit_code"><![CDATA[
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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15 @VOCDIR_COMMAND@
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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16 #for $input_file in $cooc_file
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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17 #set $cooc_ext = $input_file.ext
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18 #end for
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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19 cooc-pubmut
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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20 -m '$vocdir'
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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21 -a '$amplicons'
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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22 #if $cooc_ext == 'json'
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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23 -j '$cooc_file'
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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24 #else if $cooc_ext == 'yaml'
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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25 -y '$cooc_file'
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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26 #end if
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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27 -o cooc-table.csv
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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28 -q
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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29 $escape
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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30 #if $add_html
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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31 && pandoc cooc-table.csv -o cooc-table.html
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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32 && mkdir -p '$html.files_path'
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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33 && cp cooc-table.html '$html.files_path'
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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34 #end if
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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35 ]]></command>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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36 <inputs>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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37 <expand macro="vocdir_input"/>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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38 <param name="amplicons" type="data" format="yaml" label="List of query amplicons"
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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39 help="File generated by the Cojac mutbamscan tool"/>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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40 <param name="cooc_file" type="data" format="json,yaml" multiple="true"
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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41 label="Results generated by mutbamscan"/>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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42 <param argument="--escape" type="boolean" truevalue="--escape" falsevalue=""
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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43 checked="false" label="Use escape characters for newlines"/>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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44 <param name="add_html" type="boolean" checked="false"
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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45 label="Convert CSV output table to HTML format"/>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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46 </inputs>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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47 <outputs>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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48 <data name="table" format="csv"
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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49 label="${tool.name} on ${on_string}: Mutation cooccurrence (CSV table)"
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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50 from_work_dir="cooc-table.csv">
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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51 </data>
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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52 <data name="html" format="html"
faaae22ddea8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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53 label="${tool.name} on ${on_string}: Mutation cooccurrence (HTML)"
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54 from_work_dir="cooc-table.html">
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55 <filter>add_html</filter>
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56 </data>
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57 </outputs>
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58 <tests>
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59 <test expect_num_outputs="1">
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60 <conditional name="vocdir_option">
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61 <param name="choice" value="custom"/>
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62 <param name="voc_file" value="omicron_ba1_mutations.yaml"/>
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63 </conditional>
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64 <param name="amplicons" value="amplicons111.yaml"/>
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65 <param name="cooc_file" value="cooc-test111.json"/>
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66 <output name="table" ftype="csv">
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67 <assert_contents>
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68 <has_text text="Amplicon 76"/>
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69 <has_text text="Amplicon 81"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73 </tests>
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74 <help><![CDATA[
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75 @HELP_HEADER@
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76
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77 Information about **cooc-pubmut** method
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78 ========================================
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79
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80 The method renders a JSON or YAML file to a table as in the publication.
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81 You need to open the output CSV in a spreadsheet that understands linebreaks.
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82
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83 ]]></help>
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84 <expand macro="citations"/>
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85 </tool>