Mercurial > repos > iuc > dram_strainer

annotate dram_strainer.xml @ 2:0fc8251d3d0b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dram commit 3234c3d93fa294fa9c2c5148eae4b399d42904d8
author iuc
date Fri, 23 Aug 2024 08:17:28 +0000
parents 8a30a4bd0aaa
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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>
2
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6 <expand macro="bio_tools"/>
0
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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 strainer
2
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10 --input_tsv '$input_tsv'
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11 --input_fasta '$input_fasta'
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12 --output_fasta '$output_fasta'
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13 #if $advanced.fastas:
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14 --fastas '$advanced.fastas'
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15 #end if
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16 #if $advanced.scaffolds:
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17 --scaffolds '$advanced.scaffolds'
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18 #end if
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19 #if $advanced.genes:
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20 --genes '$advanced.genes'
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21 #end if
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22 #if $advanced.identifiers:
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23 --identifiers '$advanced.identifiers'
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24 #end if
2
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25 #if $advanced.categories:
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26 --categories '$advanced.categories'
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27 #end if
0
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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>
2
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33 <param argument="--input_tsv" 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 <expand macro="categories_param"/>
0
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46 </section>
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47 </inputs>
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48 <outputs>
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49 <data name="output_fasta" format="fasta"/>
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50 </outputs>
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51 <tests>
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52 <test expect_num_outputs="1">
2
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53 <param name="input_tsv" value="annotated1.tabular" ftype="tabular"/>
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54 <param name="input_fasta" value="strainer_input_fasta1.fasta.gz" ftype="fasta.gz"/>
0
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55 <param name="fastas" value="dataset_"/>
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56 <param name="scaffolds" value="scaffold_"/>
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57 <param name="identifiers" value="K15023"/>
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58 <param name="custom_distillate" value="distill_custom.tabular" ftype="tabular"/>
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59 <output name="output_fasta" ftype="fasta" value="strainer_output1.fasta"/>
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60 </test>
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61 </tests>
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62 <help>
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63 **What it does**
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64
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65 @WHATITDOESHEADER@
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66
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67 This tool accepts a tabular file with all gene annotations from Pfam, UniProt, dbCAN and MEROPS databases produced by the
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68 DRAM annotate tool and strains them, further analyzing genes of interest by making trees of functional models.
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69
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70 @CUSTOMDISTILLATEFILES@
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71
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72 **Options**
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73
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74 * **Space-separated list of fastas to keep** - space-separated list of fastas to keep
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75 * **Space-separated list of scaffolds to keep** - space-separated list of scaffolds to keep
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76 * **Space-separated list of genes to keep** - space-separated list of genes to keep
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77 * **Database identifiers** - database identifiers to keep
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78
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79 @WHATITDOESFOOTER@
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80 </help>
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81 <expand macro="citations"/>
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82 </tool>