Mercurial > repos > iuc > tooldistillator
annotate tooldistillator.xml @ 2:a7387ce2a8ca draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
author | iuc |
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date | Wed, 03 Jul 2024 12:06:58 +0000 |
parents | 65a69de1e294 |
children | 8d6686664021 |
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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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
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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
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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 $tool.select_tool.tool_list |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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19 --hid '$tool.select_tool.input.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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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
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22 --reference_database_version '$tool.select_tool.reference_database_version' |
1
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
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23 #if $tool.select_tool.tool_list == 'amrfinderplus': |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
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24 #if $tool.select_tool.point_mutation_report_path |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
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25 --point_mutation_report_path '$tool.select_tool.point_mutation_report_path' |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
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26 --point_mutation_report_hid '$tool.select_tool.point_mutation_report_path.hid' |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
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27 #end if |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
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28 #if $tool.select_tool.nucleotide_sequence_path |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
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29 --nucleotide_sequence_path '$tool.select_tool.nucleotide_sequence_path' |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
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30 --nucleotide_sequence_hid '$tool.select_tool.nucleotide_sequence_path.hid' |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
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31 #end if |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
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32 #elif $tool.select_tool.tool_list == 'bakta' |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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33 #if $tool.select_tool.annotation_tabular_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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34 --annotation_tabular_path '$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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35 --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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36 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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37 #if $tool.select_tool.annotation_genbank_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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38 --annotation_genbank_path '$tool.select_tool.annotation_genbank_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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39 --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
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40 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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41 #if $tool.select_tool.annotation_embl_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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42 --annotation_embl_path '$tool.select_tool.annotation_embl_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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43 --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
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44 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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45 #if $tool.select_tool.contig_sequences_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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46 --contig_sequences_path '$tool.select_tool.contig_sequences_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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47 --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
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48 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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49 #if $tool.select_tool.nucleotide_annotation_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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50 --nucleotide_annotation_path '$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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51 --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
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52 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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53 #if $tool.select_tool.amino_acid_annotation_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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54 --amino_acid_annotation_path '$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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55 --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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56 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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57 #if $tool.select_tool.summary_result_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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58 --summary_result_path '$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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59 --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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60 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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61 #if $tool.select_tool.gff_file_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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62 --gff_file_path '$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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63 --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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64 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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65 #if $tool.select_tool.hypothetical_protein_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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66 --hypothetical_protein_path '$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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67 --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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68 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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69 #if $tool.select_tool.hypothetical_tabular_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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70 --hypothetical_tabular_path '$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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71 --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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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 #if $tool.select_tool.plot_file_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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74 --plot_file_path '$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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75 --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
parents:
diff
changeset
|
76 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
77 #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
parents:
diff
changeset
|
78 #if $tool.select_tool.bandage_plot_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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79 --bandage_plot_path '$tool.select_tool.bandage_plot_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
80 --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
parents:
diff
changeset
|
81 #end if |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
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changeset
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82 #elif $tool.select_tool.tool_list == 'bwa': |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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changeset
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83 #if $tool.select_tool.paired_second_file_path |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
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84 --paired_second_file_path '$tool.select_tool.paired_second_file_path' |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
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85 --paired_second_file_hid '$tool.select_tool.paired_second_file_path.hid' |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
86 #end if |
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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87 #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
parents:
diff
changeset
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88 #if $tool.select_tool.kraken_report_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
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89 --kraken_report_path '$tool.select_tool.kraken_report_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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90 --kraken_report_hid '$tool.select_tool.kraken_report_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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91 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
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92 --threshold '$tool.select_tool.threshold' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
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93 --read_len '$tool.select_tool.read_len' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
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94 --level '$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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95 #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
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96 #if $tool.select_tool.trimmed_forward_R1_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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97 --trimmed_forward_R1_path '$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
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diff
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98 --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
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99 #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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100 #if $tool.select_tool.trimmed_reverse_R2_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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101 --trimmed_reverse_R2_path '$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
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diff
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102 --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:
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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 $tool.select_tool.html_report_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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diff
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105 --html_report_path '$tool.select_tool.html_report_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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106 --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
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107 #end if |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
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108 #elif $tool.select_tool.tool_list == 'fastqc': |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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109 #if $tool.select_tool.html_report_path |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
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110 --html_report_path '$tool.select_tool.html_report_path' |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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111 --html_report_hid '$tool.select_tool.html_report_path.hid' |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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112 #end if |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
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113 #elif $tool.select_tool.tool_list == 'flye': |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
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114 #if $tool.select_tool.contig_graph_path |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
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115 --contig_graph_path '$tool.select_tool.contig_graph_path' |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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116 --contig_graph_hid '$tool.select_tool.contig_graph_path.hid' |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
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117 #end if |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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118 #if $tool.select_tool.tsv_file_path |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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119 --tsv_file_path '$tool.select_tool.tsv_file_path' |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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120 --tsv_file_hid '$tool.select_tool.tsv_file_path.hid' |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
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121 #end if |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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122 #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:
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123 #if $tool.select_tool.summary_file_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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124 --summary_file_path '$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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125 --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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126 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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127 #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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128 #if $tool.select_tool.summary_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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129 --summary_path '$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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130 --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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131 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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132 #if $tool.select_tool.annotation_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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133 --annotation_path '$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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134 --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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135 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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136 #if $tool.select_tool.orf_fna_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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137 --orf_fna_path '$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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138 --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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139 #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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140 #if $tool.select_tool.orf_faa_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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141 --orf_faa_path '$tool.select_tool.orf_faa_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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142 --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
parents:
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143 #end if |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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144 #if $tool.select_tool.is_fna_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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145 --is_fna_path '$tool.select_tool.is_fna_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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146 --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
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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 #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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149 #if $tool.select_tool.seq_classification_file_path |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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150 --seq_classification_file_path '$tool.select_tool.seq_classification_file_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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151 --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
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152 #end if |
6e868bf6c38e
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153 #elif $tool.select_tool.tool_list == 'plasmidfinder': |
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154 #if $tool.select_tool.plasmid_result_tabular_path |
6e868bf6c38e
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155 --plasmid_result_tabular_path '$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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156 --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
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157 #end if |
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158 #if $tool.select_tool.genome_hit_path |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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159 --genome_hit_path '$tool.select_tool.genome_hit_path' |
6e868bf6c38e
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160 --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
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161 #end if |
6e868bf6c38e
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162 #if $tool.select_tool.plasmid_hit_path |
6e868bf6c38e
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163 --plasmid_hit_path '$tool.select_tool.plasmid_hit_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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164 --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
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165 #end if |
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166 #elif $tool.select_tool.tool_list == 'quast': |
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167 #if $tool.select_tool.quast_html_path |
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168 --quast_html_path '$tool.select_tool.quast_html_path' |
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169 --quast_html_hid '$tool.select_tool.quast_html_path.hid' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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170 #end if |
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171 #elif $tool.select_tool.tool_list == 'recentrifuge': |
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172 #if $tool.select_tool.rcf_stat_path |
6e868bf6c38e
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173 --rcf_stat_path '$tool.select_tool.rcf_stat_path' |
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174 --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
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175 #end if |
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176 #if $tool.select_tool.rcf_html_path |
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177 --rcf_html_path '$tool.select_tool.rcf_html_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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178 --rcf_html_hid '$tool.select_tool.rcf_html_path.hid' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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179 #end if |
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180 #elif $tool.select_tool.tool_list == 'shovill': |
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181 #if $tool.select_tool.contig_graph_path |
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182 --contig_graph_path '$tool.select_tool.contig_graph_path' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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183 --contig_graph_hid '$tool.select_tool.contig_graph_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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184 #end if |
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185 #if $tool.select_tool.bam_file_path |
6e868bf6c38e
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186 --bam_file_path '$tool.select_tool.bam_file_path' |
6e868bf6c38e
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187 --bam_file_hid '$tool.select_tool.bam_file_path.hid' |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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188 #end if |
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189 #elif $tool.select_tool.tool_list == 'staramr': |
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190 #if $tool.select_tool.mlst_file_path |
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191 --mlst_file_path '$tool.select_tool.mlst_file_path' |
6e868bf6c38e
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192 --mlst_file_hid '$tool.select_tool.mlst_file_path.hid' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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193 #end if |
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194 #if $tool.select_tool.plasmidfinder_file_path |
6e868bf6c38e
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195 --plasmidfinder_file_path '$tool.select_tool.plasmidfinder_file_path' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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196 --plasmidfinder_file_hid '$tool.select_tool.plasmidfinder_file_path.hid' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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197 #end if |
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198 #if $tool.select_tool.pointfinder_file_path |
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199 --pointfinder_file_path '$tool.select_tool.pointfinder_file_path' |
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200 --pointfinder_file_hid '$tool.select_tool.pointfinder_file_path.hid' |
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201 #end if |
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202 #if $tool.select_tool.setting_file_path |
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203 --setting_file_path '$tool.select_tool.setting_file_path' |
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204 --setting_file_hid '$tool.select_tool.setting_file_path.hid' |
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205 #end if |
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206 #elif $tool.select_tool.tool_list == 'tabular_file': |
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207 --analysis_software_name '$tool.select_tool.analysis_software_name' |
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208 #end if |
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209 -o 'tooldistillator_folder/$($tool.select_tool.tool_list)_$(i)_output.json' |
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210 | tee '$logfile' |
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211 #if $i < $counter |
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212 && |
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213 #end if |
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214 #end for |
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215 ]]> |
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216 </command> |
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217 <inputs> |
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218 <section name="tool_section" title="Available tools" expanded="true"> |
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219 <repeat name="tools" title="Tool" min="0"> |
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220 <conditional name="select_tool"> |
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221 <param name="tool_list" type="select" label="Available tools"> |
1
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222 <option value="abricate">Abricate</option> |
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223 <option value="amrfinderplus">AMRFinderPlus</option> |
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224 <option value="bakta">Bakta</option> |
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225 <option value="bandage">Bandage</option> |
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226 <option value="bracken">Bracken</option> |
2
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227 <option value="bwa">BWA</option> |
1
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228 <option value="fastp">Fastp</option> |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
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229 <option value="fastqc">Fastqc</option> |
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230 <option value="filtlong">Filtlong</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
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231 <option value="flye">Flye</option> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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232 <option value="integronfinder2">Integronfinder2</option> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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233 <option value="isescan">ISEScan</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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234 <option value="kraken2">Kraken2</option> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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235 <option value="multiqc">MultiQC</option> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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236 <option value="plasmidfinder">PlasmidFinder</option> |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
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237 <option value="polypolish">Polypolish</option> |
1
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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238 <option value="quast">Quast</option> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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239 <option value="recentrifuge">Recentrifuge</option> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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240 <option value="refseqmasher">RefSeqMasher</option> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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241 <option value="shovill">Shovill</option> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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242 <option value="staramr">Staramr</option> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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243 <option value="tabular_file">tabular_generic_file</option> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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244 </param> |
6e868bf6c38e
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245 <when 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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246 <param name="input" type="data" format="tabular" multiple="false" label="Abricate report file" help="Tabular file from abricate output"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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247 <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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248 <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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249 </when> |
1
65a69de1e294
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250 <when value="amrfinderplus"> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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251 <param name="input" type="data" format="tabular" multiple="false" label="AMRFinderPlus report file" help="Tabular file from AMRFinderPlus output"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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252 <param argument="--point_mutation_report_path" type="data" format="tabular" multiple="false" optional="true" label="AMRFinderPlus point mutation report file" help="AMRFinderPlus Tabular point mutation report file"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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253 <param argument="--nucleotide_sequence_path" type="data" format="fasta" multiple="false" optional="true" label="AMRFinderPlus nucleotide identified sequence fasta file" help="AMRFinderPlus nucleotide identified sequence fasta file"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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254 <expand macro="analysis_software_version"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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255 <expand macro="reference_database_version"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
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256 </when> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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257 <when value="bakta"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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258 <param name="input" type="data" format="json" multiple="false" label="Bakta report file" help="Json file from bakta output"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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259 <param argument="--annotation_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Bakta annotation file" help="Tabular annotation file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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260 <param argument="--annotation_genbank_path" type="data" format="txt" multiple="false" optional="true" label="Bakta genbank file" help="Genbank annotation file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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261 <param argument="--annotation_embl_path" type="data" format="txt" multiple="false" optional="true" label="Bakta embl file" help="EMBL annotation file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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262 <param argument="--contig_sequences_path" type="data" format="fasta" multiple="false" optional="true" label="Contig sequences" help="Contig sequences files"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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263 <param argument="--hypothetical_protein_path" type="data" format="fasta" multiple="false" optional="true" label="Hypothetical protein" help="Hypothetical protein fasta file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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264 <param argument="--hypothetical_tabular_path" type="data" format="tabular" multiple="false" optional="true" label="Hypothetical annotation" help="Hypothetical protein annotation"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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265 <param argument="--plot_file_path" type="data" format="svg" multiple="false" optional="true" label="Plot file" help="Plot of the annotation in svg format"/> |
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_result_path" type="data" format="txt" multiple="false" optional="true" label="Bakta summary file" help="Summary file from bakta output"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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267 <param argument="--nucleotide_annotation_path" type="data" format="fasta" multiple="false" optional="true" label="Bakta nucleotide annotation" help="Nucleotide sequence annotation file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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268 <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
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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269 <param argument="--gff_file_path" type="data" format="gff3" multiple="false" optional="true" label="Bakta annotation file" help="Annotation file in gff"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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270 <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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271 <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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272 </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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273 <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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274 <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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275 <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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276 <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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277 <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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278 </when> |
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279 <when value="bracken"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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280 <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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281 <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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282 <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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283 <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"/> |
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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 <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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285 <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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286 <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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287 <option value="D">Domain</option> |
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288 <option value="P">Phylum</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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289 <option value="C">Class</option> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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290 <option value="O">Order</option> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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291 <option value="F">Family</option> |
6e868bf6c38e
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292 <option value="G">Genus</option> |
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293 <option value="S">Species</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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294 <option value="S+">Subspecies</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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295 </param> |
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296 </when> |
2
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
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297 <when value="bwa"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
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298 <param name="input" type="data" format="bam" multiple="false" label="BWA bam file" help="Bam file from BWA output"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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299 <param argument="--paired_second_file_path" type="data" format="bam" multiple="false" optional="true" label="BWA second bam file" help="If paired inputs are used for BWA"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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300 <expand macro="analysis_software_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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301 <expand macro="reference_database_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
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302 </when> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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303 <when value="fastp"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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changeset
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304 <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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305 <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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306 <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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307 <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
iuc
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changeset
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308 <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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changeset
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309 <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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310 </when> |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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311 <when value="fastqc"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
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312 <param name="input" type="data" format="txt,tabular" multiple="false" label="Fastqc report file" help="Fastqc result in txt format"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
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313 <param argument="--html_report_path" type="data" format="html" multiple="false" optional="true" label="Fastqc report html" help="Fastqc result in html format"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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changeset
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314 <expand macro="analysis_software_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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315 <expand macro="reference_database_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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316 </when> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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317 <when value="filtlong"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
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318 <param name="input" type="data" format="fastq,fastq.gz" multiple="false" label="Filtered long reads from Filtlong" help="Filtlong reads in fastq format"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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changeset
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319 <expand macro="analysis_software_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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changeset
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320 <expand macro="reference_database_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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321 </when> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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322 <when value="flye"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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323 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from assembly"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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324 <param argument="--contig_graph_path" type="data" format="html" multiple="false" optional="true" label="Flye Graphical Fragment Assembly file" help="Assembly graph file from Flye"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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325 <param argument="--tsv_file_path" type="data" format="txt,tabular" multiple="false" optional="true" label="Flye Assembly info file" help="Assembly info file from Flye"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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changeset
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326 <expand macro="analysis_software_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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327 <expand macro="reference_database_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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328 </when> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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changeset
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329 <when value="integronfinder2"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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changeset
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330 <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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331 <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
iuc
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changeset
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332 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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changeset
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333 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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334 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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diff
changeset
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335 <when value="isescan"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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336 <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
iuc
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changeset
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337 <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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338 <param argument="--annotation_path" type="data" format="gff" optional="true" multiple="false" label="annotation results" help="Annotation in gff file format"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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339 <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
iuc
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340 <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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341 <param argument="--is_fna_path" type="data" format="fasta" optional="true" multiple="false" label="IS fna file" help="Nuleotide sequence to the inserted elements"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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342 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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343 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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344 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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345 <when value="kraken2"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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346 <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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347 <param argument="--seq_classification_file_path" type="data" format="txt,tabular" optional="true" multiple="false" label="Sequence assignation" help="Reads assignation file"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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348 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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349 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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350 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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351 <when value="multiqc"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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352 <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
iuc
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353 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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354 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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355 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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changeset
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356 <when value="plasmidfinder"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
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357 <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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358 <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
iuc
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359 <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
iuc
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360 <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
iuc
parents:
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changeset
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361 <expand macro="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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changeset
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362 <expand macro="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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changeset
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363 </when> |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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364 <when value="polypolish"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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changeset
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365 <param name="input" type="data" format="fasta" multiple="false" label="Contigs file" help="Contig fasta file from Polypolish"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
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366 <expand macro="analysis_software_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
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367 <expand macro="reference_database_version"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
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368 </when> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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369 <when value="quast"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
370 <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
iuc
parents:
diff
changeset
|
371 <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
iuc
parents:
diff
changeset
|
372 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
373 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
374 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
375 <when value="recentrifuge"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
376 <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
iuc
parents:
diff
changeset
|
377 <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
iuc
parents:
diff
changeset
|
378 <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
iuc
parents:
diff
changeset
|
379 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
380 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
381 </when> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
382 <when value="refseqmasher"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
383 <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
iuc
parents:
diff
changeset
|
384 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
385 <expand macro="reference_database_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
386 </when> |
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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387 <when value="shovill"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
388 <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
iuc
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changeset
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389 <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
iuc
parents:
diff
changeset
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390 <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
iuc
parents:
diff
changeset
|
391 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
392 <expand macro="reference_database_version"/> |
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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393 </when> |
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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394 <when value="staramr"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
395 <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
iuc
parents:
diff
changeset
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396 <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
iuc
parents:
diff
changeset
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397 <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
iuc
parents:
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changeset
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398 <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
iuc
parents:
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changeset
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399 <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
iuc
parents:
diff
changeset
|
400 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
401 <expand macro="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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changeset
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402 </when> |
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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403 <when value="tabular_file"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
404 <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
iuc
parents:
diff
changeset
|
405 <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
iuc
parents:
diff
changeset
|
406 <expand macro="analysis_software_version"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
407 <expand macro="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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changeset
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408 </when> |
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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409 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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410 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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changeset
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411 </section> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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changeset
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412 <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
iuc
parents:
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413 </inputs> |
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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414 <outputs> |
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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415 <collection name="output_json" type="list" label="${tool.name} on ${on_string}: JSON"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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416 <discover_datasets pattern="(?P<designation>.+)\.json" format="json" directory="tooldistillator_folder" /> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
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417 </collection> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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418 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: Log"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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419 <filter> log == True </filter> |
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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420 </data> |
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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421 </outputs> |
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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422 <tests> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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changeset
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423 <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
iuc
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424 <section name="tool_section"> |
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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425 <repeat name="tools"> |
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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426 <conditional name="select_tool"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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427 <param name="tool_list" value="abricate"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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428 <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
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429 <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
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430 <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
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431 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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432 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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433 </section> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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434 <param name="log" value="true"/> |
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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435 <output_collection name="output_json" type="list"> |
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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436 <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:
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changeset
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437 </output_collection> |
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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438 <output name="logfile" compare="sim_size" > |
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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439 <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
iuc
parents:
diff
changeset
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440 </output> |
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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441 </test> |
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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442 <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
iuc
parents:
diff
changeset
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443 <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
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444 <repeat name="tools"> |
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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445 <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
|
446 <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
|
447 <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
|
448 <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
|
449 <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
|
450 <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
|
451 <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
|
452 <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
|
453 <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
|
454 <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
|
455 <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
|
456 <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
|
457 <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
|
458 <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
|
459 <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
|
460 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
461 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
462 </section> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
463 <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
|
464 <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
|
465 </output_collection> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
466 </test> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
467 <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
|
468 <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
|
469 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
470 <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
|
471 <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
|
472 <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
|
473 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
474 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
475 </section> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
476 <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
|
477 <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
|
478 </output_collection> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
479 </test> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
480 <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
|
481 <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
|
482 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
483 <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
|
484 <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
|
485 <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
|
486 <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
|
487 <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
|
488 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
489 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
490 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
491 <conditional name="select_tool"> |
1
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
492 <param name="tool_list" value="amrfinderplus"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
493 <param name="input" value="amrfinderplus/AMRFinderPlus_report.tsv" ftype="tabular"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
494 <param name="point_mutation_report_path" value="amrfinderplus/AMRFinderPlus_Point_mutation_report.tsv" ftype="tabular"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
495 <param name="nucleotide_sequence_path" value="amrfinderplus/AMRFinderPlus_Nucleotide_identified_sequences.fasta" ftype="fasta"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
496 <param name="analysis_software_version" value="3.11.26"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
497 <param name="reference_database_version" value="v3.11-2023-04-17.1"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
498 </conditional> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
499 </repeat> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
500 <repeat name="tools"> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
501 <conditional name="select_tool"> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
502 <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
|
503 <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
|
504 <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
|
505 <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
|
506 <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
|
507 <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
|
508 <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
|
509 <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
|
510 <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
|
511 <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
|
512 <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
|
513 <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
|
514 <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
|
515 <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
|
516 <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
|
517 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
518 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
519 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
520 <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
|
521 <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
|
522 <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
|
523 <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
|
524 <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
|
525 <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
|
526 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
527 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
528 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
529 <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
|
530 <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
|
531 <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
|
532 <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
|
533 <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
|
534 <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
|
535 <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
|
536 <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
|
537 <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
|
538 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
539 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
540 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
541 <conditional name="select_tool"> |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
542 <param name="tool_list" value="bwa"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
543 <param name="input" value="bwa/aligned_R1.bam" ftype="bam"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
544 <param name="paired_second_file_path" value="bwa/aligned_R1.bam"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
545 <param name="analysis_software_version" value="2.2.1"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
546 <param name="reference_database_version" value="tests/data/dummy/flye/assembly.fasta"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
547 </conditional> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
548 </repeat> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
549 <repeat name="tools"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
550 <conditional name="select_tool"> |
0
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="fastp"/> |
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="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
|
553 <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
|
554 <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
|
555 <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
|
556 <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
|
557 <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
|
558 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
559 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
560 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
561 <conditional name="select_tool"> |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
562 <param name="tool_list" value="fastqc"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
563 <param name="input" value="fastqc/fastqc_report.txt" ftype="txt"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
564 <param name="html_report_path" value="fastqc/fastqc_report.html"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
565 <param name="analysis_software_version" value="0.12.1"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
566 <param name="reference_database_version" value=""/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
567 </conditional> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
568 </repeat> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
569 <repeat name="tools"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
570 <conditional name="select_tool"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
571 <param name="tool_list" value="filtlong"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
572 <param name="input" value="filtlong/filtered_sample.fastq.gz" ftype="fastq.gz"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
573 <param name="analysis_software_version" value="0.2.1"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
574 <param name="reference_database_version" value=""/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
575 </conditional> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
576 </repeat> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
577 <repeat name="tools"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
578 <conditional name="select_tool"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
579 <param name="tool_list" value="flye"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
580 <param name="input" value="flye/assembly.fasta" ftype="fasta"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
581 <param name="contig_graph_path" value="flye/assembly.gfa" ftype="txt"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
582 <param name="tsv_file_path" value="flye/assembly_infos.tsv" ftype="tabular"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
583 <param name="analysis_software_version" value="2.9.1"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
584 <param name="reference_database_version" value=""/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
585 </conditional> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
586 </repeat> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
587 <repeat name="tools"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
588 <conditional name="select_tool"> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
589 <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
|
590 <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
|
591 <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
|
592 <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
|
593 <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
|
594 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
595 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
596 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
597 <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
|
598 <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
|
599 <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
|
600 <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
|
601 <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
|
602 <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
|
603 <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
|
604 <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
|
605 <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
|
606 <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
|
607 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
608 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
609 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
610 <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
|
611 <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
|
612 <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
|
613 <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
|
614 <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
|
615 <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
|
616 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
617 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
618 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
619 <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
|
620 <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
|
621 <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
|
622 <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
|
623 <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
|
624 <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
|
625 <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
|
626 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
627 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
628 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
629 <conditional name="select_tool"> |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
630 <param name="tool_list" value="polypolish"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
631 <param name="input" value="polypolish/polished_assembly.fasta" ftype="fasta"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
632 <param name="analysis_software_version" value="0.2.1"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
633 <param name="reference_database_version" value=""/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
634 </conditional> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
635 </repeat> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
636 <repeat name="tools"> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
637 <conditional name="select_tool"> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
638 <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
|
639 <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
|
640 <param name="quast_html_path" value="quast/quast_report.html"/> |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
641 <param name="analysis_software_version" value="0.5.0"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
642 <param name="reference_database_version" value=""/> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
643 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
644 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
645 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
646 <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
|
647 <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
|
648 <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
|
649 <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
|
650 <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
|
651 <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
|
652 <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
|
653 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
654 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
655 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
656 <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
|
657 <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
|
658 <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
|
659 <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
|
660 <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
|
661 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
662 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
663 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
664 <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
|
665 <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
|
666 <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
|
667 <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
|
668 <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
|
669 <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
|
670 <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
|
671 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
672 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
673 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
674 <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
|
675 <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
|
676 <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
|
677 <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
|
678 <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
|
679 <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
|
680 <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
|
681 <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
|
682 <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
|
683 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
684 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
685 <repeat name="tools"> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
686 <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
|
687 <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
|
688 <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
|
689 <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
|
690 <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
|
691 <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
|
692 </conditional> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
693 </repeat> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
694 </section> |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
695 <output_collection name="output_json" type="list" count="21"> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
696 <expand macro="element_assert" name="abricate_0_output" text="Enterococcus faecalis V583"/> |
1
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
697 <expand macro="element_assert" name="amrfinderplus_1_output" text="mercury resistance transcriptional regulator MerR"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
698 <expand macro="element_assert" name="bakta_2_output" text="hypothetical protein"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
699 <expand macro="element_assert" name="bandage_3_output" text="3042326"/> |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
700 <expand macro="element_assert" name="bracken_4_output" text="Staphylococcus_aureus"/> |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
701 <expand macro="element_assert" name="bwa_5_output" text="bwa_report"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
702 <expand macro="element_assert" name="fastp_6_output" text="705053822"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
703 <expand macro="element_assert" name="fastqc_7_output" text="Sequences flagged as poor quality"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
704 <expand macro="element_assert" name="filtlong_8_output" text="filtlong_report"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
705 <expand macro="element_assert" name="flye_9_output" text="contig_2"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
706 <expand macro="element_assert" name="integronfinder2_10_output" text="2353.0"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
707 <expand macro="element_assert" name="isescan_11_output" text="IS200/IS605"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
708 <expand macro="element_assert" name="kraken2_12_output" text="Enterococcus_faecalis"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
709 <expand macro="element_assert" name="plasmidfinder_13_output" text="repUS40_1_repB"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
710 <expand macro="element_assert" name="polypolish_14_output" text="320811"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
711 <expand macro="element_assert" name="quast_15_output" text="2944723"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
712 <expand macro="element_assert" name="recentrifuge_16_output" text="6.4917947578"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
713 <expand macro="element_assert" name="refseqmasher_17_output" text="GCF_000519925.1"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
714 <expand macro="element_assert" name="shovill_18_output" text="436224"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
715 <expand macro="element_assert" name="staramr_19_output" text="10_Enterococcus_faecalis_S17_L001"/> |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
716 <expand macro="element_assert" name="tabular_file_20_output" text="NP_814691"/> |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
717 </output_collection> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
718 </test> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
719 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
720 </tests> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
721 <help><![CDATA[ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
722 **What it does** |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
723 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
724 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
|
725 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
726 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
|
727 ** Tool input** |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
728 |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
729 ToolDistillator can use several input type from at least 21 different tools and 1 generic tool for tabular file: |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
730 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
731 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
732 | Tools | Version | Default input file| Optional files | |
1
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
733 +----------------+----------------+-------------------+------------------------------------------------------------+ |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
734 | 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
|
735 +----------------+----------------+-------------------+------------------------------------------------------------+ |
1
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
736 | AMRFinderPlus | 3.11.26 | report.tsv | point_mutation_report.tsv, nucleotide_sequence.fasta | |
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
|
737 +----------------+----------------+-------------------+------------------------------------------------------------+ |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
738 | 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
iuc
parents:
diff
changeset
|
739 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
740 | Bandage | 0.8.1 | info.txt | | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
741 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
742 | Bracken | 2.8 | output.tsv | taxonomy.tsv | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
743 +----------------+----------------+-------------------+------------------------------------------------------------+ |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
744 | BWA | 2.2.1 | input1.bam | input2.bam | |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
745 +----------------+----------------+-------------------+------------------------------------------------------------+ |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
746 | Fastp | 0.23.2 | output.json | | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
747 +----------------+----------------+-------------------+------------------------------------------------------------+ |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
748 | Fastqc | 0.12.1 | report.txt | report.html | |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
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749 +----------------+----------------+-------------------+------------------------------------------------------------+ |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
750 | Filtlong | 0.2.1 | input.fastq | | |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
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751 +----------------+----------------+-------------------+------------------------------------------------------------+ |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
752 | Flye | 2.9.1 | contig.fasta | contig.gfa, infos.tsv | |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
753 +----------------+----------------+-------------------+------------------------------------------------------------+ |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
754 | 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
iuc
parents:
diff
changeset
|
755 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
756 | 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
iuc
parents:
diff
changeset
|
757 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
758 | 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
iuc
parents:
diff
changeset
|
759 +----------------+----------------+-------------------+------------------------------------------------------------+ |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
|
760 | MultiQC | 1.11 | report.html | no optional files | |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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1
diff
changeset
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761 +----------------+----------------+-------------------+------------------------------------------------------------+ |
1
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
changeset
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762 | PlasmidFinder | 2.1.6 | output.json | genome_hits.fasta, plasmid_hits.fasta | |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
763 +----------------+----------------+-------------------+------------------------------------------------------------+ |
2
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
parents:
1
diff
changeset
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764 | Polypolish | 0.5.0 | contig.fasta | | |
a7387ce2a8ca
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit d7cada7ddf775e946e218fdc839e6e4c8aac6d80
iuc
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765 +----------------+----------------+-------------------+------------------------------------------------------------+ |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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changeset
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766 | Quast | 5.2.0 | output.tsv | | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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changeset
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767 +----------------+----------------+-------------------+------------------------------------------------------------+ |
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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768 | 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
iuc
parents:
diff
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769 +----------------+----------------+-------------------+------------------------------------------------------------+ |
1
65a69de1e294
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 30f10306f4283140f7e54cfe1b8bc1f76f4ef834
iuc
parents:
0
diff
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770 | RefSeqMasher | 0.1.2 | output.tsv | | |
0
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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diff
changeset
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771 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
772 | 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
iuc
parents:
diff
changeset
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773 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
774 | 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
iuc
parents:
diff
changeset
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775 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
776 | tabular_file | 0 | output.tsv | no optional files | |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
777 +----------------+----------------+-------------------+------------------------------------------------------------+ |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
778 |
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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|
779 ** Options ** |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
780 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
781 You can add a tool version and a database version for related tools. |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
782 For some tools you can add optional files previously produced by the tool |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
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changeset
|
783 |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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changeset
|
784 ]]></help> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
parents:
diff
changeset
|
785 <expand macro="citations"/> |
6e868bf6c38e
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tooldistillator commit 491c6fc94851aab68cb7529dd6b6fbc6caa84bf2
iuc
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|
786 </tool> |