Mercurial > repos > iuc > dram_strainer

annotate dram_strainer.xml @ 1:8a30a4bd0aaa draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit e0934fc66bfd742731505cacd18cbf53b26d4f2a
author iuc
date Tue, 11 Jul 2023 23:44:41 +0000
parents e945bfed58b9
children 0fc8251d3d0b
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1 <tool id="dram_strainer" name="DRAM strain annotations" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
0
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2 <description>down to 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>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 DRAM.py strainer
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9 --input_annotations '$input_annotations'
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10 --input_fasta '$input_fasta'
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11 --output_fasta '$output_fasta'
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12 #if $advanced.fastas:
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13 --fastas '$advanced.fastas'
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14 #end if
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15 #if $advanced.scaffolds:
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16 --scaffolds '$advanced.scaffolds'
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17 #end if
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18 #if $advanced.genes:
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19 --genes '$advanced.genes'
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20 #end if
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21 #if $advanced.identifiers:
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22 --identifiers '$advanced.identifiers'
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23 #end if
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24 ## Broken in 3.5.1 - https://github.com/WrightonLabCSU/DRAM/issues/194
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25 ##if $advanced.categories:
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26 ## --categories '$advanced.categories'
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27 ##end if
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28 #if $advanced.custom_distillate:
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29 --custom_distillate '$advanced.custom_distillate'
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30 #end if
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31 ]]></command>
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32 <inputs>
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33 <param argument="--input_annotations" type="data" format="tabular" label="Annotations file" help="Produced by the DRAM annotate tool"/>
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34 <param argument="--input_fasta" type="data" format="fasta,fasta.gz" label="FASTA file to filter"/>
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35 <section name="advanced" title="Advanced options" expanded="false">
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36 <param argument="--fastas" type="text" value="" label="Space-separated list of fastas to keep" help="Optional, leave blank to ignore">
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37 <expand macro="sanitizer"/>
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38 </param>
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39 <param argument="--scaffolds" type="text" value="" label="Space-separated list of scaffolds to keep" help="Optional, leave blank to ignore">
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40 <expand macro="sanitizer"/>
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41 </param>
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42 <expand macro="genes_param"/>
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43 <expand macro="identifiers_param"/>
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44 <expand macro="custom_distillate_param"/>
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45 <!-- Broken in 3.5.1, see above -->
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46 <!-- <expand macro="categories_param"/> -->
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47 </section>
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48 </inputs>
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49 <outputs>
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50 <data name="output_fasta" format="fasta"/>
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51 </outputs>
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52 <tests>
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53 <test expect_num_outputs="1">
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54 <param name="input_annotations" ftype="tabular" value="annotated1.tabular"/>
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55 <param name="input_fasta" ftype="fasta.gz" value="strainer_input_fasta1.fasta.gz"/>
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56 <param name="fastas" value="dataset_"/>
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57 <param name="scaffolds" value="scaffold_"/>
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58 <param name="identifiers" value="K15023"/>
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59 <param name="custom_distillate" ftype="tabular" value="distill_custom.tabular"/>
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60 <output name="output_fasta" ftype="fasta" value="strainer_output1.fasta"/>
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61 </test>
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62 </tests>
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63 <help>
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64 **What it does**
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65
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66 @WHATITDOESHEADER@
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67
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68 This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the
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69 DRAM annotate tool and strains them, further analyzing genes of interest by making trees of functional models.
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70
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71 @CUSTOMDISTILLATEFILES@
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72
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73 **Options**
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74
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75 * **Space-separated list of fastas to keep** - space-separated list of fastas to keep
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76 * **Space-separated list of scaffolds to keep** - space-separated list of scaffolds to keep
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77 * **Space-separated list of genes to keep** - space-separated list of genes to keep
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78 * **Database identifiers** - database identifiers to keep
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79
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80 @WHATITDOESFOOTER@
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81 </help>
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82 <expand macro="citations"/>
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83 </tool>