Mercurial > repos > iuc > tooldistillator
annotate tooldistillator.xml @ 0:6e868bf6c38e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
author | iuc |
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date | Tue, 30 Apr 2024 08:42:33 +0000 |
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children | 65a69de1e294 |
rev | line source |
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0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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1 <tool id="tooldistillator" name="ToolDistillator" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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2 <description> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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3 Extract information from output files of specific tools and expose it as JSON files |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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4 </description> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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5 <macros> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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6 <import>macro.xml</import> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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changeset
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7 </macros> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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8 <expand macro="biotools"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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9 <expand macro="requirements"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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10 <expand macro="version_command"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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11 <command detect_errors="aggressive"><![CDATA[ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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12 #import re |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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13 mkdir "tooldistillator_folder" && |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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14 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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15 #set $counter = len($tool_section.tools)-1 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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16 #for $i, $tool in enumerate( $tool_section.tools ) |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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17 tooldistillator |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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18 $tool.select_tool.tool_list |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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19 --hid '$tool.select_tool.input.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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20 '$tool.select_tool.input' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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21 --analysis_software_version '$tool.select_tool.analysis_software_version' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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22 --reference_database_version '$tool.select_tool.reference_database_version' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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23 #if $tool.select_tool.tool_list == 'bakta' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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24 #if $tool.select_tool.annotation_tabular_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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25 --annotation_tabular_path '$tool.select_tool.annotation_tabular_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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26 --annotation_tabular_hid '$tool.select_tool.annotation_tabular_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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27 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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28 #if $tool.select_tool.annotation_genbank_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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29 --annotation_genbank_path '$tool.select_tool.annotation_genbank_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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30 --annotation_genbank_hid '$tool.select_tool.annotation_genbank_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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31 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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32 #if $tool.select_tool.annotation_embl_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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33 --annotation_embl_path '$tool.select_tool.annotation_embl_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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34 --annotation_embl_hid '$tool.select_tool.annotation_embl_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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35 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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36 #if $tool.select_tool.contig_sequences_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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37 --contig_sequences_path '$tool.select_tool.contig_sequences_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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38 --contig_sequences_hid '$tool.select_tool.contig_sequences_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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39 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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40 #if $tool.select_tool.nucleotide_annotation_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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41 --nucleotide_annotation_path '$tool.select_tool.nucleotide_annotation_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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42 --nucleotide_annotation_hid '$tool.select_tool.nucleotide_annotation_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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43 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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44 #if $tool.select_tool.amino_acid_annotation_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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45 --amino_acid_annotation_path '$tool.select_tool.amino_acid_annotation_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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46 --amino_acid_annotation_hid '$tool.select_tool.amino_acid_annotation_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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47 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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48 #if $tool.select_tool.summary_result_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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49 --summary_result_path '$tool.select_tool.summary_result_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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50 --summary_result_hid '$tool.select_tool.summary_result_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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51 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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52 #if $tool.select_tool.gff_file_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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53 --gff_file_path '$tool.select_tool.gff_file_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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54 --gff_file_hid '$tool.select_tool.gff_file_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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55 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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56 #if $tool.select_tool.hypothetical_protein_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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57 --hypothetical_protein_path '$tool.select_tool.hypothetical_protein_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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58 --hypothetical_protein_hid '$tool.select_tool.hypothetical_protein_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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59 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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60 #if $tool.select_tool.hypothetical_tabular_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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61 --hypothetical_tabular_path '$tool.select_tool.hypothetical_tabular_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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62 --hypothetical_tabular_hid '$tool.select_tool.hypothetical_tabular_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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63 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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64 #if $tool.select_tool.plot_file_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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65 --plot_file_path '$tool.select_tool.plot_file_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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66 --plot_file_hid '$tool.select_tool.plot_file_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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67 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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68 #elif $tool.select_tool.tool_list == 'bandage': |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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69 #if $tool.select_tool.bandage_plot_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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70 --bandage_plot_path '$tool.select_tool.bandage_plot_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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71 --bandage_plot_hid '$tool.select_tool.bandage_plot_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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72 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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73 #elif $tool.select_tool.tool_list == 'bracken': |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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74 #if $tool.select_tool.kraken_report_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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75 --kraken_report_path '$tool.select_tool.kraken_report_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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76 --kraken_report_hid '$tool.select_tool.kraken_report_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
77 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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78 --threshold '$tool.select_tool.threshold' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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79 --read_len '$tool.select_tool.read_len' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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80 --level '$tool.select_tool.level' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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81 #elif $tool.select_tool.tool_list == 'fastp': |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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82 #if $tool.select_tool.trimmed_forward_R1_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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83 --trimmed_forward_R1_path '$tool.select_tool.trimmed_forward_R1_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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84 --trimmed_forward_R1_hid '$tool.select_tool.trimmed_forward_R1_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
85 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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86 #if $tool.select_tool.trimmed_reverse_R2_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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87 --trimmed_reverse_R2_path '$tool.select_tool.trimmed_reverse_R2_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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88 --trimmed_reverse_R2_hid '$tool.select_tool.trimmed_reverse_R2_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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89 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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90 #if $tool.select_tool.html_report_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
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91 --html_report_path '$tool.select_tool.html_report_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
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92 --html_report_hid '$tool.select_tool.html_report_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
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93 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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94 #elif $tool.select_tool.tool_list == 'integronfinder2': |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
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95 #if $tool.select_tool.summary_file_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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96 --summary_file_path '$tool.select_tool.summary_file_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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diff
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97 --summary_file_hid '$tool.select_tool.summary_file_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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98 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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99 #elif $tool.select_tool.tool_list == 'isescan': |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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100 #if $tool.select_tool.summary_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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101 --summary_path '$tool.select_tool.summary_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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102 --summary_hid '$tool.select_tool.summary_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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103 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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104 #if $tool.select_tool.annotation_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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105 --annotation_path '$tool.select_tool.annotation_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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106 --annotation_hid '$tool.select_tool.annotation_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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107 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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108 #if $tool.select_tool.orf_fna_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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109 --orf_fna_path '$tool.select_tool.orf_fna_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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110 --orf_fna_hid '$tool.select_tool.orf_fna_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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111 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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112 #if $tool.select_tool.orf_faa_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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113 --orf_faa_path '$tool.select_tool.orf_faa_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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114 --orf_faa_hid '$tool.select_tool.orf_faa_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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115 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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116 #if $tool.select_tool.is_fna_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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117 --is_fna_path '$tool.select_tool.is_fna_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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118 --is_fna_hid '$tool.select_tool.is_fna_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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119 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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120 #elif $tool.select_tool.tool_list == 'kraken2': |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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121 #if $tool.select_tool.seq_classification_file_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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122 --seq_classification_file_path '$tool.select_tool.seq_classification_file_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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123 --seq_classification_file_hid '$tool.select_tool.seq_classification_file_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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124 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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125 #elif $tool.select_tool.tool_list == 'plasmidfinder': |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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126 #if $tool.select_tool.plasmid_result_tabular_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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127 --plasmid_result_tabular_path '$tool.select_tool.plasmid_result_tabular_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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128 --plasmid_result_tabular_hid '$tool.select_tool.plasmid_result_tabular_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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129 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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130 #if $tool.select_tool.genome_hit_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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131 --genome_hit_path '$tool.select_tool.genome_hit_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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132 --genome_hit_hid '$tool.select_tool.genome_hit_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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133 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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134 #if $tool.select_tool.plasmid_hit_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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135 --plasmid_hit_path '$tool.select_tool.plasmid_hit_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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136 --plasmid_hit_hid '$tool.select_tool.plasmid_hit_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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137 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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138 #elif $tool.select_tool.tool_list == 'quast': |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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139 #if $tool.select_tool.quast_html_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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140 --quast_html_path '$tool.select_tool.quast_html_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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141 --quast_html_hid '$tool.select_tool.quast_html_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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142 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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143 #elif $tool.select_tool.tool_list == 'recentrifuge': |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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144 #if $tool.select_tool.rcf_stat_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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145 --rcf_stat_path '$tool.select_tool.rcf_stat_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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146 --rcf_stat_hid '$tool.select_tool.rcf_stat_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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147 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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148 #if $tool.select_tool.rcf_html_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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149 --rcf_html_path '$tool.select_tool.rcf_html_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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150 --rcf_html_hid '$tool.select_tool.rcf_html_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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151 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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152 #elif $tool.select_tool.tool_list == 'shovill': |
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153 #if $tool.select_tool.contig_graph_path |
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154 --contig_graph_path '$tool.select_tool.contig_graph_path' |
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155 --contig_graph_hid '$tool.select_tool.contig_graph_path.hid' |
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156 #end if |
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157 #if $tool.select_tool.bam_file_path |
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158 --bam_file_path '$tool.select_tool.bam_file_path' |
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159 --bam_file_hid '$tool.select_tool.bam_file_path.hid' |
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160 #end if |
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161 #elif $tool.select_tool.tool_list == 'staramr': |
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162 #if $tool.select_tool.mlst_file_path |
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163 --mlst_file_path '$tool.select_tool.mlst_file_path' |
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164 --mlst_file_hid '$tool.select_tool.mlst_file_path.hid' |
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165 #end if |
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166 #if $tool.select_tool.plasmidfinder_file_path |
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167 --plasmidfinder_file_path '$tool.select_tool.plasmidfinder_file_path' |
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168 --plasmidfinder_file_hid '$tool.select_tool.plasmidfinder_file_path.hid' |
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169 #end if |
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170 #if $tool.select_tool.pointfinder_file_path |
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171 --pointfinder_file_path '$tool.select_tool.pointfinder_file_path' |
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172 --pointfinder_file_hid '$tool.select_tool.pointfinder_file_path.hid' |
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173 #end if |
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174 #if $tool.select_tool.setting_file_path |
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175 --setting_file_path '$tool.select_tool.setting_file_path' |
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176 --setting_file_hid '$tool.select_tool.setting_file_path.hid' |
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177 #end if |
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178 #elif $tool.select_tool.tool_list == 'tabular_file': |
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179 --analysis_software_name '$tool.select_tool.analysis_software_name' |
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180 #end if |
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181 -o 'tooldistillator_folder/$($tool.select_tool.tool_list)_$(i)_output.json' |
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182 | tee '$logfile' |
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183 #if $i < $counter |
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184 && |
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185 #end if |
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186 #end for |
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187 ]]> |
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188 </command> |
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189 <inputs> |
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190 <section name="tool_section" title="Available tools" expanded="true"> |
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191 <repeat name="tools" title="Tool" min="0"> |
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192 <conditional name="select_tool"> |
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193 <param name="tool_list" type="select" label="Available tools"> |
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194 <option value="abricate">abricate</option> |
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195 <option value="bakta">bakta</option> |
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196 <option value="bandage">bandage</option> |
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197 <option value="bracken">bracken</option> |
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198 <option value="fastp">fastp</option> |
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199 <option value="integronfinder2">integronfinder2</option> |
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200 <option value="isescan">isescan</option> |
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201 <option value="kraken2">kraken2</option> |
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202 <option value="multiqc">MultiQC</option> |
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203 <option value="plasmidfinder">plasmidfinder</option> |
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204 <option value="quast">quast</option> |
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205 <option value="recentrifuge">recentrifuge</option> |
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206 <option value="refseqmasher">refseqmasher</option> |
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207 <option value="shovill">shovill</option> |
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208 <option value="staramr">staramr</option> |
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209 <option value="tabular_file">tabular_generic_file</option> |
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210 </param> |
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211 <when value="abricate"> |
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212 <param name="input" type="data" format="tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/> |
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213 <expand macro="analysis_software_version"/> |
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214 <expand macro="reference_database_version"/> |
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215 </when> |
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216 <when value="bakta"> |
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217 <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/> |
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218 <param argument="--annotation_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Bakta annotation file" help="Tabular annotation file"/> |
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219 <param argument="--annotation_genbank_path" type="data" format="txt" multiple="false" optional="true" label="Bakta genbank file" help="Genbank annotation file"/> |
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220 <param argument="--annotation_embl_path" type="data" format="txt" multiple="false" optional="true" label="Bakta embl file" help="EMBL annotation file"/> |
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221 <param argument="--contig_sequences_path" type="data" format="fasta" multiple="false" optional="true" label="Contig sequences" help="Contig sequences files"/> |
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222 <param argument="--hypothetical_protein_path" type="data" format="fasta" multiple="false" optional="true" label="Hypothetical protein" help="Hypothetical protein fasta file"/> |
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223 <param argument="--hypothetical_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Hypothetical annotation" help="Hypothetical protein annotation"/> |
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224 <param argument="--plot_file_path" type="data" format="svg" multiple="false" optional="true" label="Plot file" help="Plot of the annotation in svg format"/> |
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225 <param argument="--summary_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/> |
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226 <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide annotation" help="Nucleotide sequence annotation file"/> |
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227 <param argument="--amino_acid_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta protein annotation" help="Amino acid sequence annotation file"/> |
6e868bf6c38e
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228 <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file in gff"/> |
6e868bf6c38e
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229 <expand macro="analysis_software_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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230 <expand macro="reference_database_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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231 </when> |
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232 <when value="bandage"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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233 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bandage report file" help="Tabular file from bandage output"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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234 <param argument="--bandage_plot_path" type="data" format="svg" multiple="false" optional="true" label="Bandage plot" help="Bandage visualisation file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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235 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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236 <expand macro="reference_database_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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237 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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238 <when value="bracken"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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239 <param name="input" type="data" format="txt,tabular" multiple="false" label="Bracken report file" help="Tabular file from bracken output"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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240 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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241 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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242 <param argument="--kraken_report_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Kraken re-estimated report" help="New kraken report from bracken tool"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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243 <param argument="--threshold" type="integer" min="0" optional="true" label="PRIOR on read numbers" help="Prior of read for estimation, default is 0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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244 <param argument="--read_len" type="integer" min="0" optional="true" label="Read length"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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245 <param argument="--level" type="select" label="Taxonomic level estimation" optional="true" help="Level of final abundance (from Domain to subspecies, default on species)"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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246 <option value="D">Domain</option> |
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247 <option value="P">Phylum</option> |
6e868bf6c38e
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248 <option value="C">Class</option> |
6e868bf6c38e
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249 <option value="O">Order</option> |
6e868bf6c38e
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250 <option value="F">Family</option> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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251 <option value="G">Genus</option> |
6e868bf6c38e
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252 <option value="S">Species</option> |
6e868bf6c38e
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253 <option value="S+">Subspecies</option> |
6e868bf6c38e
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254 </param> |
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255 </when> |
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256 <when value="fastp"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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257 <param name="input" type="data" format="json" multiple="false" label="Fastp report file" help="Fastp result in json format"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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258 <param argument="--trimmed_forward_R1_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R1" help="trimmed file R1"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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259 <param argument="--trimmed_reverse_R2_path" type="data" format="fastq,fastq.gz" optional="true" multiple="false" label="Fastp trimmed R2" help="trimmed file R2"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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260 <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastp report html" help="Fastp result in html format"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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261 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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262 <expand macro="reference_database_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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263 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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264 <when value="integronfinder2"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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265 <param name="input" type="data" format="txt,tabular" multiple="false" label="Integronfinder report" help="Integron file from integronfinder2"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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266 <param argument="--summary_file_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Summary report" help="Summary file from integronfinder2"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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267 <expand macro="analysis_software_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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268 <expand macro="reference_database_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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269 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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270 <when value="isescan"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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271 <param name="input" type="data" format="txt,tabular" multiple="false" label="Isescan report" help="IseScan file from integronfinder2"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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272 <param argument="--summary_path" type="data" format="tabular" optional="true" multiple="false" label="summary file" help="ISEscan summary"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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273 <param argument="--annotation_path" type="data" format="gff" optional="true" multiple="false" label="annotation results" help="Annotation in gff file format"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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274 <param argument="--orf_fna_path" type="data" format="fasta" optional="true" multiple="false" label="ORF fna file" help="Nuleotide sequence to the ORFs"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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275 <param argument="--orf_faa_path" type="data" format="fasta" optional="true" multiple="false" label="ORF faa file" help="Amino acid sequence to the ORFs"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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276 <param argument="--is_fna_path" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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277 <expand macro="analysis_software_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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278 <expand macro="reference_database_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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279 </when> |
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280 <when value="kraken2"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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281 <param name="input" type="data" format="txt,tabular" multiple="false" label="kraken report" help="Taxonomic assignation file from kraken2"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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282 <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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283 <expand macro="analysis_software_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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284 <expand macro="reference_database_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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285 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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286 <when value="multiqc"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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287 <param name="input" type="data" format="html" multiple="false" label="MultiQC report" help="Html report from MultiQC"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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288 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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289 <expand macro="reference_database_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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290 </when> |
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291 <when value="plasmidfinder"> |
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292 <param name="input" type="data" format="json" multiple="false" label="Json report" help="Plasmidfinder result from json file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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293 <param argument="--plasmid_result_tabular_path" type="data" format="tabular" optional="true" multiple="false" label="Result in tabular format" help="Plasmid result in tabular format"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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294 <param argument="--genome_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Genome hits" help="Sequence hit in the analyzed genome"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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295 <param argument="--plasmid_hit_path" type="data" format="fasta" optional="true" multiple="false" label="Plasmid hits" help="Plasmid sequence identified"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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296 <expand macro="analysis_software_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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297 <expand macro="reference_database_version"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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298 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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299 <when value="quast"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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300 <param name="input" type="data" format="txt,tabular" multiple="false" label="Quast report" help="Tabular Quast report"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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301 <param argument="--quast_html_path" type="data" format="html" multiple="false" optional="true" label="Quast html report" help="Quast html report"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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302 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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303 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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304 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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305 <when value="recentrifuge"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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306 <param name="input" type="data" format="txt,tabular" multiple="false" label="Recentrifuge data file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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307 <param argument="--rcf_stat_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Recentrifuge stat file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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308 <param argument="--rcf_html_path" type="data" format="html" optional="true" multiple="false" label="Recentrifuge html report file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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309 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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310 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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311 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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312 <when value="refseqmasher"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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313 <param name="input" type="data" format="txt,tabular" multiple="false" label="RefsesMasher results"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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314 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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315 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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316 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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317 <when value="shovill"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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318 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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319 <param argument="--contig_graph_path" type="data" format="txt" optional="true" multiple="false" label="Contig graph file" help="Graphic file assembly"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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320 <param argument="--bam_file_path" type="data" format="bam" optional="true" multiple="false" label="Bam file" help="Alignemnt file in bam format"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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321 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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322 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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323 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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324 <when value="staramr"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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325 <param name="input" type="data" format="txt,tabular" multiple="false" label="Resfinder report" help="Resfinder result from starAMR"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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326 <param argument="--mlst_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="MLST results" help="mlst scheme file result from starAMR"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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327 <param argument="--plasmidfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Plasmid results" help="Plasmidfinder result from starAMR"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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328 <param argument="--pointfinder_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Pointfinder results" help="PointFinder result from starAMR"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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329 <param argument="--setting_file_path" type="data" optional="true" format="txt,tabular" multiple="false" label="Setting informations" help="Settings file from starAMR"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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330 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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331 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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332 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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333 <when value="tabular_file"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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334 <param name="input" type="data" format="txt,tabular" multiple="false" label="Tabular file type" help="Generic result file in tabular format with header"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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335 <param argument="--analysis_software_name" type="text" multiple="false" optional="true" label="Tool name" help="Tool name which generated the result file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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336 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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337 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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338 </when> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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339 </conditional> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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340 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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341 </section> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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342 <param name="log" type="boolean" truevalue="true" falsevalue="" label="Add log" help="Activate/Deactivate the log"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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343 </inputs> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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344 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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345 <collection name="output_json" type="list" label="${tool.name} on ${on_string}: JSON"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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346 <discover_datasets pattern="(?P<designation>.+)\.json" format="json" directory="tooldistillator_folder" /> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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347 </collection> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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348 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: Log"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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349 <filter> log == True </filter> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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350 </data> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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351 </outputs> |
6e868bf6c38e
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352 <tests> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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353 <test expect_num_outputs="2"> <!-- TEST_1 abricate with logfile --> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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354 <section name="tool_section"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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355 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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356 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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357 <param name="tool_list" value="abricate"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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358 <param name="input" value="abricate/report.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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359 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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360 <param name="reference_database_version" value="2.0" /> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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361 </conditional> |
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362 </repeat> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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363 </section> |
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364 <param name="log" value="true"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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365 <output_collection name="output_json" type="list"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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366 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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367 </output_collection> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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368 <output name="logfile" compare="sim_size" > |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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369 <assert_contents><has_size value="0"/></assert_contents> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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370 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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371 </test> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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372 <test expect_num_outputs="1"> <!-- TEST_2 bakta all files --> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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373 <section name="tool_section"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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374 <repeat name="tools"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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375 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
376 <param name="tool_list" value="bakta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
377 <param name="input" value="bakta/bakta.json" ftype="json"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
378 <param name="annotation_tabular_path" value="bakta/bakta_summary.txt" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
379 <param name="annotation_genbank_path" value="bakta/bakta_summary.txt" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
380 <param name="annotation_embl_path" value="bakta/bakta_summary.txt" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
381 <param name="contig_sequences_path" value="bakta/bakta_summary.txt" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
382 <param name="hypothetical_protein_path" value="bakta/bakta_summary.txt" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
383 <param name="hypothetical_tabular_path" value="bakta/bakta_summary.txt" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
384 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
385 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide_annotation.ffn" ftype="fasta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
386 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
387 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
388 <param name="analysis_software_version" value="1.8.1"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
389 <param name="reference_database_version" value="5.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
390 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
391 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
392 </section> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
393 <output_collection name="output_json" type="list" count="1"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
394 <expand macro="element_assert" name="bakta_0_output" text="hypothetical protein"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
395 </output_collection> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
396 </test> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
397 <test expect_num_outputs="1"> <!-- TEST_3 bakta with no files --> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
398 <section name="tool_section"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
399 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
400 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
401 <param name="tool_list" value="bakta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
402 <param name="input" value="bakta/bakta.json" ftype="json"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
403 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
404 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
405 </section> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
406 <output_collection name="output_json" type="list" count="1"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
407 <expand macro="element_assert" name="bakta_0_output" text="hypothetical protein"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
408 </output_collection> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
409 </test> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
410 <test expect_num_outputs="1"> <!-- TEST_4 All tool in repeat --> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
411 <section name="tool_section"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
412 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
413 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
414 <param name="tool_list" value="abricate"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
415 <param name="input" value="abricate/report.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
416 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
417 <param name="reference_database_version" value="2.0" /> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
418 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
419 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
420 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
421 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
422 <param name="tool_list" value="bakta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
423 <param name="input" value="bakta/bakta.json" ftype="json"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
424 <param name="annotation_tabular_path" value="bakta/bakta_annotation.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
425 <param name="annotation_genbank_path" value="bakta/bakta_gbff.gbff"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
426 <param name="annotation_embl_path" value="bakta/bakta_embl.embl"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
427 <param name="contig_sequences_path" value="bakta/bakta_contigs_sequences.fna" ftype="fasta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
428 <param name="hypothetical_protein_path" value="bakta/bakta_hypothetical.faa" ftype="fasta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
429 <param name="hypothetical_tabular_path" value="bakta/bakta_hypothetical.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
430 <param name="plot_file_path" value="bakta/bakta_plot.svg"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
431 <param name="summary_result_path" value="bakta/bakta_summary.txt" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
432 <param name="nucleotide_annotation_path" value="bakta/bakta_nucleotide_annotation.ffn" ftype="fasta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
433 <param name="amino_acid_annotation_path" value="bakta/bakta_aminoacid.faa" ftype="fasta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
434 <param name="gff_file_path" value="bakta/bakta_annotation.gff3" ftype="gff3"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
435 <param name="analysis_software_version" value="1.8.1"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
436 <param name="reference_database_version" value="5.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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437 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
438 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
439 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
440 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
441 <param name="tool_list" value="bandage"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
442 <param name="input" value="bandage/bandage_info.txt" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
443 <param name="bandage_plot_path" value="bandage/bandage_plot.svg"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
444 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
445 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
446 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
447 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
448 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
449 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
450 <param name="tool_list" value="bracken"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
451 <param name="input" value="bracken/bracken_report.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
452 <param name="kraken_report_path" value="bracken/bracken_kraken_report.tsv"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
453 <param name="read_len" value="100"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
454 <param name="level" value="S"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
455 <param name="threshold" value="1"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
456 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
457 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
458 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
459 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
460 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
461 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
462 <param name="tool_list" value="fastp"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
463 <param name="input" value="fastp/fastp_report.json" ftype="json"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
464 <param name="trimmed_forward_R1_path" value="fastp/trimmed_R1.fastq.gz"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
465 <param name="trimmed_reverse_R2_path" value="fastp/trimmed_R2.fastq.gz"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
466 <param name="html_report_path" value="fastp/fastp_report.html"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
467 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
468 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
469 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
470 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
471 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
472 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
473 <param name="tool_list" value="integronfinder2"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
474 <param name="input" value="integronfinder2/results.integrons" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
475 <param name="summary_file_path" value="integronfinder2/results.summary" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
476 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
477 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
478 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
479 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
480 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
481 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
482 <param name="tool_list" value="isescan"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
483 <param name="input" value="isescan/results.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
484 <param name="summary_path" value="isescan/summary.tsv"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
485 <param name="annotation_path" value="isescan/annotation.gff"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
486 <param name="orf_fna_path" value="isescan/orf.fna"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
487 <param name="orf_faa_path" value="isescan/orf.faa"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
488 <param name="is_fna_path" value="isescan/is.fna"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
489 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
490 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
491 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
492 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
493 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
494 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
495 <param name="tool_list" value="kraken2"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
496 <param name="input" value="kraken2/taxonomy_report.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
497 <param name="seq_classification_file_path" value="kraken2/taxonomy_result.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
498 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
499 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
500 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
501 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
502 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
503 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
504 <param name="tool_list" value="plasmidfinder"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
505 <param name="input" value="plasmidfinder/plasmidfinder_result.json" ftype="json"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
506 <param name="genome_hit_path" value="plasmidfinder/genome_hit.fasta" ftype="fasta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
507 <param name="plasmid_hit_path" value="plasmidfinder/plasmid_hit.fasta" ftype="fasta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
508 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
509 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
510 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
511 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
512 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
513 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
514 <param name="tool_list" value="quast"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
515 <param name="input" value="quast/quast_result.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
516 <param name="quast_html_path" value="quast/quast_report.html"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
517 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
518 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
519 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
520 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
521 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
522 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
523 <param name="tool_list" value="recentrifuge"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
524 <param name="input" value="recentrifuge/rcf_data.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
525 <param name="rcf_stat_path" value="recentrifuge/rcf_stat.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
526 <param name="rcf_html_path" value="recentrifuge/rcf_report.html"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
527 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
528 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
529 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
530 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
531 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
532 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
533 <param name="tool_list" value="refseqmasher"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
534 <param name="input" value="refseqmasher/refsesqmasher.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
535 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
536 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
537 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
538 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
539 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
540 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
541 <param name="tool_list" value="shovill"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
542 <param name="input" value="shovill/contigs.fa" ftype="fasta"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
543 <param name="contig_graph_path" value="shovill/contigs.gfa" ftype="txt"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
544 <param name="bam_file_path" value="shovill/alignment.bam" ftype="bam"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
545 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
546 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
547 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
548 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
549 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
550 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
551 <param name="tool_list" value="staramr"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
552 <param name="input" value="staramr/resfinder.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
553 <param name="mlst_file_path" value="staramr/mlst.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
554 <param name="plasmidfinder_file_path" value="staramr/plasmidfinder.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
555 <param name="pointfinder_file_path" value="staramr/pointfinder.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
556 <param name="setting_file_path" value="staramr/settings.txt" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
557 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
558 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
559 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
560 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
561 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
562 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
563 <param name="tool_list" value="tabular_file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
564 <param name="input" value="tabular_file/report.tsv" ftype="tabular"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
565 <param name="analysis_software_name" value="test_galaxy"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
566 <param name="analysis_software_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
567 <param name="reference_database_version" value="1.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
568 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
569 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
570 </section> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
571 <output_collection name="output_json" type="list" count="15"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
572 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
573 <expand macro="element_assert" name="bakta_1_output" text="hypothetical protein"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
574 <expand macro="element_assert" name="bandage_2_output" text="3042326"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
575 <expand macro="element_assert" name="bracken_3_output" text="Staphylococcus_aureus"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
576 <expand macro="element_assert" name="fastp_4_output" text="705053822"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
577 <expand macro="element_assert" name="integronfinder2_5_output" text="2353.0"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
578 <expand macro="element_assert" name="isescan_6_output" text="IS200/IS605"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
579 <expand macro="element_assert" name="kraken2_7_output" text="Enterococcus_faecalis"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
580 <expand macro="element_assert" name="plasmidfinder_8_output" text="repUS40_1_repB"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
581 <expand macro="element_assert" name="quast_9_output" text="2944723"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
582 <expand macro="element_assert" name="recentrifuge_10_output" text="6.4917947578"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
583 <expand macro="element_assert" name="refseqmasher_11_output" text="GCF_000519925.1"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
584 <expand macro="element_assert" name="shovill_12_output" text="436224"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
585 <expand macro="element_assert" name="staramr_13_output" text="10_Enterococcus_faecalis_S17_L001"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
586 <expand macro="element_assert" name="tabular_file_14_output" text="NP_814691"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
587 </output_collection> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
588 </test> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
589 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
590 </tests> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
591 <help><![CDATA[ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
592 **What it does** |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
593 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
594 ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools. |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
595 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
596 This tool here is extracting information from output files of specific tools and exposing it as JSON files |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
597 ** Tool input** |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
598 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
599 ToolDistillator can use several input type from at least 14 different tools : |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
600 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
601 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
602 | Tools | Version | Default input file| Optional files | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
603 | Abricate | 1.0.1 | output.tsv | | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
604 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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605 | Bakta | 1.7.0 | output.json | protein.faa, nucleotide.fna, annotation.gff3, summary.txt | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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606 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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607 | Bandage | 0.8.1 | info.txt | | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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608 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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609 | Bracken | 2.8 | output.tsv | taxonomy.tsv | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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610 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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611 | Fastp | 0.23.2 | output.json | | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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612 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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613 | Integronfinder2| 2.0.2 | output.integrons | output.summary | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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614 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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615 | ISEScan | 1.7.2.3 | output.tsv | is.fna, orf.faa, orf.fna | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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616 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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617 | Kraken2 | 2.1.2 | taxonomy.tsv | reads_assignation.txt | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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618 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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619 | Plasmidfinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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620 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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621 | Quast | 5.2.0 | output.tsv | | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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622 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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623 | Recentrifuge | 1.10.0 | data.tsv | report.html, stat.tsv | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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624 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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625 | Refseqmasher | 0.1.2 | output.tsv | | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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626 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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627 | Shovill | 1.1.0 | contigs.fasta | alignment.bam, contigs.gfa | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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628 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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629 | Staramr | 0.9.1 | resfinder.tsv | mlst.tsv, pointfinder.tsv, plasmidfinder.tsv, settings.tsv | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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630 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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631 | tabular_file | 0 | output.tsv | no optional files | |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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632 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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633 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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634 ** Options ** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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635 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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636 You can add a tool version and a database version for related tools. |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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637 For some tools you can add optional files previously produced by the tool |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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638 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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639 ]]></help> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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640 <expand macro="citations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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641 </tool> |