Mercurial > repos > iuc > cooc_tabmut
annotate cooc_tabmut.xml @ 0:4be399803856 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
author | iuc |
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date | Thu, 11 Aug 2022 13:50:09 +0000 |
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children | 579538ff939d |
rev | line source |
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0
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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1 <tool id="cooc_tabmut" name="Cojac: tabmut" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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2 profile="@PROFILE@"> |
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3 <description> |
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4 export cooccurrence mutations as a table |
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5 </description> |
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6 <macros> |
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7 <import>macros.xml</import> |
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8 </macros> |
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9 <expand macro="biotools"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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10 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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11 <expand macro="version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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12 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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13 #for $input_file in $cooc_file |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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14 #set $cooc_ext = $input_file.ext |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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15 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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16 cooc-tabmut |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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17 #if $cooc_ext == 'json' |
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18 -j '$cooc_file' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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19 #else if $cooc_ext == 'yaml' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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20 -y '$cooc_file' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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21 #end if |
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22 -o cooc-table.csv |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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23 #if $table_orientation.choice == 'lines' |
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24 -l |
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25 #else if $table_orientation.choice == 'multiindex' |
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26 -m |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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27 #end if |
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28 -q |
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29 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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30 <inputs> |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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31 <param name="cooc_file" type="data" format="json,yaml" multiple="true" |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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32 label="Results generated by mutbamscan"/> |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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33 <conditional name="table_orientation"> |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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34 <param name="choice" type="select" label="Output table orientation"> |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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35 <option value="columns">Column-oriented table (default)</option> |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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36 <option value="lines">Line-oriented table</option> |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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37 <option value="multiindex">Multi-level indexing (amplicons and counts |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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38 categories) |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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39 </option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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40 </param> |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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41 <when value="columns"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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42 <when value="lines"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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43 <when value="multiindex"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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44 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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45 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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46 <outputs> |
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47 <data name="table" format="csv" |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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48 label="${tool.name} on ${on_string}: Mutation cooccurrence (CSV table)" |
4be399803856
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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49 from_work_dir="cooc-table.csv"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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50 </data> |
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51 </outputs> |
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52 <tests> |
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53 <test expect_num_outputs="1"> |
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54 <param name="cooc_file" value="cooc-test111.json"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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55 <conditional name="table_orientation"> |
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56 <param name="choice" value="columns"/> |
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57 </conditional> |
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58 <output name="table" ftype="csv"> |
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59 <assert_contents> |
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60 <has_text text="A76_om1.count"/> |
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61 <has_text text="A76_om1.mut_oneless"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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62 </assert_contents> |
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63 </output> |
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64 </test> |
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65 </tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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66 <help><![CDATA[ |
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67 @HELP_HEADER@ |
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68 |
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69 Information about **cooc_tabmut** method |
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70 ======================================== |
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71 |
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72 The method exports a JSON or YAML file as a CSV/TSV table for downstream analysis (e.g.: RStudio). |
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73 |
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74 ]]></help> |
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75 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cojac commit 38ed91999d4bbe3bedc294197926ea332eb6cd5e
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76 </tool> |