Mercurial > repos > iuc > dram_neighborhoods

annotate dram_neighborhoods.xml @ 2:669459119c20 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit a5e28ac40a63a269100ddec5629aee5256ce00ef
author iuc
date Fri, 09 Feb 2024 21:36:37 +0000
parents d1f8d32bbe3b
children 877bdba8fc5d
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1 <tool id="dram_neighborhoods" name="DRAM find neighborhoods" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>around genes of interest</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
2
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 DRAM.py neighborhoods
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10 --input_file '$input_file'
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11 --output_dir 'output_dir'
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12 #if $advanced.genes:
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13 --genes '$advanced.genes'
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14 #end if
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15 #if $advanced.identifiers:
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16 --identifiers '$advanced.identifiers'
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17 #end if
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18 #if $advanced.custom_distillate:
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19 --custom_distillate '$advanced.custom_distillate'
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20 #end if
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21 ## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194
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22 ##if $advanced.categories:
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23 ## --categories '$advanced.categories'
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24 ##end if
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25 #if $advanced.genes_loc:
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26 --genes_loc '$advanced.genes_loc'
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27 #end if
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28 #if $advanced.scaffolds_loc:
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29 --scaffolds_loc '$advanced.scaffolds_loc'
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30 #end if
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31 #if $advanced.distance_genes > 0:
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32 --distance_genes $advanced.distance_genes
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33 #end if
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34 #if $advanced.distance_bp > 0:
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35 --distance_bp $advanced.distance_bp
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36 #end if
1
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37 && (test -f 'output_dir/neighborhood_annotations.tsv' && mv 'output_dir/neighborhood_annotations.tsv' '$output_neighborhood_annotations' || echo 'No neighborhood_annotations.tsv output produced')
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38 #if $advanced.genes_loc:
1
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39 && (test -f 'output_dir/neighborhood_genes.dat' && mv 'output_dir/neighborhood_genes.dat' '$output_neighborhood_genes' || echo 'No neighborhood_genes.dat output produced')
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40 #end if
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41 #if $advanced.scaffolds_loc:
1
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42 && (test -f 'output_dir/neighborhood_scaffolds.fna' && mv 'output_dir/neighborhood_scaffolds.fna' '$output_neighborhood_scaffolds' || echo 'No neighborhood_scaffolds.fna output produced')
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43 #end if
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44 ]]></command>
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45 <inputs>
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46 <expand macro="input_file_param"/>
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47 <section name="advanced" title="Advanced options" expanded="false">
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48 <expand macro="genes_param"/>
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49 <expand macro="identifiers_param"/>
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50 <expand macro="custom_distillate_param"/>
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51 <!-- Broken in 3.5.1 - see above -->
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52 <!-- <expand macro="categories_param"/> -->
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53 <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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54 <param argument="--scaffolds_loc" type="data" format="fasta" optional="true" label="File containing scaffolds to filter to neighborhoods" help="Optional, leave blank to ignore"/>
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55 <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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56 <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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57 </section>
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58 </inputs>
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59 <outputs>
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60 <data name="output_neighborhood_annotations" format="tabular" label="${tool.name} on ${on_string}: neighborhood annotations"/>
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61 <data name="output_neighborhood_genes" format="fasta" label="${tool.name} on ${on_string}: neighborhood genes">
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62 <filter>advanced['genes_loc']</filter>
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63 </data>
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64 <data name="output_neighborhood_scaffolds" format="fasta" label="${tool.name} on ${on_string}: neighborhood scaffolds">
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65 <filter>advanced['scaffolds_loc']</filter>
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66 </data>
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67 </outputs>
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68 <tests>
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69 <test expect_num_outputs="1">
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70 <param name="input_file" ftype="tabular" value="annotated1.tabular"/>
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71 <param name="distance_genes" value="10"/>
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72 <output name="output_neighborhood_annotations">
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73 <assert_contents>
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74 <has_size value="2046495" delta="1000"/>
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75 </assert_contents>
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76 <assert_contents>
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77 <has_text text="neighborhood_number"/>
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78 </assert_contents>
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79 </output>
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80 </test>
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81 <test expect_num_outputs="3">
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82 <param name="input_file" ftype="tabular" value="annotated1.tabular"/>
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83 <param name="distance_genes" value="10"/>
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84 <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/>
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85 <param name="genes_loc" ftype="fasta" value="neighborhoods_genes_loc1.fna"/>
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86 <param name="scaffolds_loc" ftype="fasta" value="neighborhoods_scaffolds_loc1.fasta"/>
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87 <output name="output_neighborhood_annotations">
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88 <assert_contents>
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89 <has_size value="2046495" delta="10000"/>
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90 </assert_contents>
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91 <assert_contents>
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92 <has_text text="neighborhood_number"/>
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93 </assert_contents>
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94 </output>
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95 <output name="output_neighborhood_genes" ftype="fasta" value="neighborhoods_output1.fasta"/>
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96 <output name="output_neighborhood_scaffolds" ftype="fasta" value="neighborhoods_output1.fasta">
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97 </output>
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98 </test>
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99 </tests>
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100 <help>
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101 **What it does**
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102
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103 @WHATITDOESHEADER@
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104
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105 This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the
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106 DRAM annotate tool and finds neighborhoods around genes of interest.
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107
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108 @CUSTOMDISTILLATEFILES@
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109
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110 **Options**
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111
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112 * **Space-separated list of genes to keep** - genee names from DRAM around which to find neighborhoods
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113 * **Database identifiers** - database identifiers assigned by DRAM around which to find neighborhoods
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114 * **File containing genes to filter to neighborhoods** - file containing genes to filter to neighborhoods
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115 * **File containing scaffolds to filter to neighborhoods** - file containing scaffolds to filter to neighborhoods
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116 * **Number of genes away from center to include in neighborhoods** - number of genes away from center to include in neighborhoods
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117 * **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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118
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119 @WHATITDOESFOOTER@
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120 </help>
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121 <expand macro="citations"/>
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122 </tool>