Mercurial > repos > iuc > dram_neighborhoods
annotate dram_neighborhoods.xml @ 0:fc93558da540 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
author | iuc |
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date | Sat, 10 Dec 2022 21:14:08 +0000 |
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children | d1f8d32bbe3b |
rev | line source |
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0
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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1 <tool id="dram_neighborhoods" name="DRAM find neighborhoods" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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2 <description>around genes of interest</description> |
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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4 <import>macros.xml</import> |
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5 </macros> |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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6 <expand macro="requirements"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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7 <command detect_errors="exit_code"><![CDATA[ |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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8 DRAM.py neighborhoods |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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9 --input_file '$input_file' |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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10 --output_dir 'output_dir' |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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11 #if $advanced.genes: |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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12 --genes '$advanced.genes' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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13 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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14 #if $advanced.identifiers: |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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15 --identifiers '$advanced.identifiers' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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16 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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17 #if $advanced.custom_distillate: |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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18 --custom_distillate '$advanced.custom_distillate' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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19 #end if |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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20 ## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194 |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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21 ##if $advanced.categories: |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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22 ## --categories '$advanced.categories' |
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23 ##end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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24 #if $advanced.genes_loc: |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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25 --genes_loc '$advanced.genes_loc' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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26 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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27 #if $advanced.scaffolds_loc: |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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28 --scaffolds_loc '$advanced.scaffolds_loc' |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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29 #end if |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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30 #if $advanced.distance_genes > 0: |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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31 --distance_genes $advanced.distance_genes |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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32 #end if |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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33 #if $advanced.distance_bp > 0: |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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34 --distance_bp $advanced.distance_bp |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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35 #end if |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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36 && test -f 'output_dir/neighborhood_annotations.tsv' && mv 'output_dir/neighborhood_annotations.tsv' '$output_neighborhood_annotations' || echo 'No neighborhood_annotations.tsv output produced' |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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37 #if $advanced.genes_loc: |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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38 && test -f 'output_dir/neighborhood_genes.dat' && mv 'output_dir/neighborhood_genes.dat' '$output_neighborhood_genes' || echo 'No neighborhood_genes.dat output produced' |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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39 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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40 #if $advanced.scaffolds_loc: |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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41 && test -f 'output_dir/neighborhood_scaffolds.fna' && mv 'output_dir/neighborhood_scaffolds.fna' '$output_neighborhood_scaffolds' || echo 'No neighborhood_scaffolds.fna output produced' |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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42 #end if |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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43 ]]></command> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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44 <inputs> |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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45 <expand macro="input_file_param"/> |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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46 <section name="advanced" title="Advanced options" expanded="false"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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47 <expand macro="genes_param"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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48 <expand macro="identifiers_param"/> |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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49 <expand macro="custom_distillate_param"/> |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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50 <!-- Broken in 3.5.1 - see above --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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51 <!-- <expand macro="categories_param"/> --> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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52 <param argument="--genes_loc" type="data" format="fasta" optional="true" label="File containing genes to filter to neighborhoods" help="Optional, leave blank to ignore"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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53 <param argument="--scaffolds_loc" type="data" format="fasta" optional="true" label="File containing scaffolds to filter to neighborhoods" help="Optional, leave blank to ignore"/> |
fc93558da540
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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54 <param argument="--distance_genes" type="integer" value="0" min="0" label="Number of genes away from center to include in neighborhoods" help="Optional, set to 0 to ignore, but must provide distance away in genes, bp or both"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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55 <param argument="--distance_bp" type="integer" value="0" min="0" label="Number of base pairs away from center to include in neighborhoods" help="Optional, set to 0 to ignore, but must provide distance away in bp, genes or both"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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56 </section> |
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57 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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58 <outputs> |
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59 <data name="output_neighborhood_annotations" format="tabular" label="${tool.name} on ${on_string}: neighborhood annotations"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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60 <data name="output_neighborhood_genes" format="fasta" label="${tool.name} on ${on_string}: neighborhood genes"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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61 <filter>advanced['genes_loc']</filter> |
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62 </data> |
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63 <data name="output_neighborhood_scaffolds" format="fasta" label="${tool.name} on ${on_string}: neighborhood scaffolds"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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64 <filter>advanced['scaffolds_loc']</filter> |
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65 </data> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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66 </outputs> |
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67 <tests> |
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68 <test expect_num_outputs="1"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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69 <param name="input_file" ftype="tabular" value="annotated1.tabular"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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70 <param name="distance_genes" value="10"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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71 <output name="output_neighborhood_annotations"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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72 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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73 <has_size value="2046495" delta="1000"/> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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74 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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75 <assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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76 <has_text text="neighborhood_number"/> |
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77 </assert_contents> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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78 </output> |
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79 </test> |
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80 <test expect_num_outputs="3"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit df10ba86507266a6a6f83c9bbefb7191a41b46f5
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81 <param name="input_file" ftype="tabular" value="annotated1.tabular"/> |
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82 <param name="distance_genes" value="10"/> |
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83 <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/> |
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84 <param name="genes_loc" ftype="fasta" value="neighborhoods_genes_loc1.fna"/> |
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85 <param name="scaffolds_loc" ftype="fasta" value="neighborhoods_scaffolds_loc1.fasta"/> |
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86 <output name="output_neighborhood_annotations"> |
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87 <assert_contents> |
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88 <has_size value="2046495" delta="10000"/> |
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89 </assert_contents> |
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90 <assert_contents> |
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91 <has_text text="neighborhood_number"/> |
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92 </assert_contents> |
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93 </output> |
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94 <output name="output_neighborhood_genes" ftype="fasta" value="neighborhoods_output1.fasta"/> |
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95 <output name="output_neighborhood_scaffolds" ftype="fasta" value="neighborhoods_output1.fasta"> |
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96 </output> |
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97 </test> |
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98 </tests> |
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99 <help> |
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100 **What it does** |
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101 |
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102 @WHATITDOESHEADER@ |
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103 |
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104 This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the |
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105 DRAM annotate tool and finds neighborhoods around genes of interest. |
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106 |
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107 @CUSTOMDISTILLATEFILES@ |
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108 |
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109 **Options** |
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110 |
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111 * **Space-separated list of genes to keep** - genee names from DRAM around which to find neighborhoods |
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112 * **Database identifiers** - database identifiers assigned by DRAM around which to find neighborhoods |
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113 * **File containing genes to filter to neighborhoods** - file containing genes to filter to neighborhoods |
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114 * **File containing scaffolds to filter to neighborhoods** - file containing scaffolds to filter to neighborhoods |
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115 * **Number of genes away from center to include in neighborhoods** - number of genes away from center to include in neighborhoods |
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116 * **Number of base pairs away from center to include in neighborhoods** - number of base pairs away from center to include in neighborhoods |
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117 |
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118 @WHATITDOESFOOTER@ |
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119 </help> |
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120 <expand macro="citations"/> |
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121 </tool> |