Mercurial > repos > gga > apollo_export

annotate export.xml @ 20:d87bd3f2654e draft default tip

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 12282c16658b37858f49944796fd95515ef0fc0b
author gga
date Wed, 11 Jan 2023 11:45:03 +0000
parents 4ba339eb4f73
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1 <?xml version="1.0"?>
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2 <tool id="export" name="Retrieve Data" version="@WRAPPER_VERSION@">
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3 <description>from Apollo into Galaxy</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <code file="webapollo.py"/>
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9 <command detect_errors="aggressive"><![CDATA[
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10 @AUTH@
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11 python '$__tool_directory__/export.py'
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13 @ORG_CN_OR_GUESS@
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14
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15 --gff '$gff_out'
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16 $gff_with_fasta
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17 --fasta_pep '$fasta_pep'
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18 --fasta_cds '$fasta_cds'
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19 --fasta_cdna '$fasta_cdna'
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20 --vcf '$vcf_out'
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21 --json '$json_out'
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22 $die
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23
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24 '$__user_email__'
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25
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26 ]]></command>
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27 <inputs>
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28 <expand macro="cn_or_guess" />
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29 <param name="gff_with_fasta" type="boolean" truevalue="--gff_with_fasta" falsevalue="" label="Include fasta in the GFF3 file" help="The fasta is available separately in the cDNA sequence file, but some tools might prefer it included in the GFF3 file."/>
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30 <param name="die" type="boolean" truevalue="--die" falsevalue="" label="Fail hard if any portion of the export fails" help="By default it will just print a warning message, this causes any error to be fatal."/>
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31 </inputs>
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32 <outputs>
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33 <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
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34 <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
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35 <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>
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36 <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/>
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37 <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/>
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38 <data format="json" name="json_out" label="Metadata from Apollo">
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39 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
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40 </data>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <conditional name="org_source">
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45 <param name="source_select" value="direct"/>
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46 <param name="org_raw" value="test_organism" />
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47 </conditional>
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48 <conditional name="cn_source">
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49 <param name="source_select" value="all"/>
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50 </conditional>
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51
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52 <output name="gff_out">
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53 <assert_contents>
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54 <has_text text="##sequence-region Merlin 1 172788" />
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55 <has_text text="owner=admin@local.host;" />
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56 </assert_contents>
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57 </output>
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58 <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
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59 <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
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60 <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>
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61 <output name="vcf_out" file="export/out.vcf" lines_diff="4"/>
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62 <output name="json_out">
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63 <assert_contents>
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64 <has_text text="test_organism" />
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65 </assert_contents>
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66 </output>
0
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 **What it does**
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71
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72 Exports the sequence data and annotations from Apollo.
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73
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74 If you provide an Apollo JSON file as input to the Organism Common Name list,
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75 this will enable extracting multiple organism's data at once from Apollo.
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76 Beware that currently all gff3 and fasta responses are merged together. If you
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77 have two separate organisms with identically named reference sequences, it will
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78 not be possible to separate those out.
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79
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80 @REFERENCES@
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81 ]]></help>
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82 <expand macro="citations"/>
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83 </tool>