annotate isescan.xml @ 1:045f2ebfe030 draft default tip

planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
author pimarin
date Tue, 23 Aug 2022 10:19:38 +0000
parents cecb2758ec26
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045f2ebfe030 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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1 <tool id="isescan" name="ISEScan" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
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2 <description> Insertion Sequence Elements detection in prokaryotic genomes </description>
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3 <macros>
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4 <import>macro.xml</import>
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5 </macros>
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6 <expand macro='xrefs'/>
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7 <expand macro="requirements" />
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8 <expand macro="version_command" />
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9 <command detect_errors="exit_code"><![CDATA[
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10 isescan.py
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11 --seqfile '$input_file'
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12 --output 'results'
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13 $remove_short_is
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14 --nthread \${GALAXY_SLOTS:-7}
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15 | tee '$logfile'
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16
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17 ]]>
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18 </command>
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19 <inputs>
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20 <param name="input_file" type="data" format="fasta,fasta.gz" label="Genome fasta input" help="Fasta sequence to analyse for IS"/>
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21 <param name="remove_short_is" argument="--removeShortIS" type="boolean" truevalue="--removeShortIS" falsevalue=""
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22 label="Remove incomplete IS elements"
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23 help="Remove partial IS elements which include IS element with length &gt; 400 or single copy IS element without perfect TIR"/>
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24 <param name="output_format" type="select" label="Output format type" help="Choose an output file format">
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25 <option value="raw"> Raw format (txt) </option>
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26 <option value="csv"> Coma separate file (CSV) </option>
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27 <option value="tsv" selected="true"> Tabular separate file (TSV) </option>
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28 </param>
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29 <param name="log_activate" type="boolean" truevalue="True" falsevalue="False" checked="True" label="Keep the log file"/>
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30 </inputs>
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31 <outputs>
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32 <data name="summary" format="txt" label="${tool.name} on ${on_string}: Summary of detected IS"/>
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33 <data name="is_results" format="tabular" label="${tool.name} on ${on_string}: IS detected">
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34 <change_format>
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35 <when input="output_format" value="raw" format="txt"/>
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36 <when input="output_format" value="csv" format="csv"/>
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37 <when input="output_format" value="tsv" format="tabular"/>
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38 </change_format>
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39 </data>
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40 <data name="gff_file" format="gff3" label="IS annotation"/>
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41 <data name="is_fasta" format="fasta" label="${tool.name} on ${on_string}: IS nucleic sequence"/>
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42 <data name="tpase_fasta" format="fasta" label="${tool.name} on ${on_string}: Transposase nucleic acid sequence"/>
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43 <data name="tpase_amino" format="fasta" label="${tool.name} on ${on_string}: Transposase amino acid sequence"/>
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44 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: Log file">
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45 <filter> log_activate == True </filter>
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46 </data>
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47 </outputs>
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48 <tests>
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49 <test> <!-- TEST_1 default parameters -->
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50 <param name="input_file" value="NC_012624.fna" />
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51 <output name="summary" value="TEST_1/test_1.fna.sum"/>
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52 <output name="is_results" value="TEST_1/test_1.fna.tsv"/>
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53 <output name="gff_file" value="TEST_1/test_1.fna.gff"/>
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54 <output name="is_fasta" value="TEST_1/test_1.fna.is.fna"/>
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55 <output name="tpase_fasta" value="TEST_1/test_1.fna.orf.fna"/>
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56 <output name="tpase_amino" value="TEST_1/test_1.fna.orf.faa"/>
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57 <output name="logfile" value="TEST_1/test_1.log" lines_diff="50"/>
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58 </test>
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59 <test> <!-- TEST_2 with remove_short_is and raw output-->
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60 <param name="input_file" value="NC_012624.fna"/>
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61 <param name="remove_short_is" value="true"/>
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62 <param name="output_format" value="raw"/>
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63 <output name="summary" value="TEST_2/test_2.fna.sum"/>
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64 <output name="is_results" value="TEST_2/test_2.fna.raw"/>
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65 <output name="gff_file" value="TEST_2/test_2.fna.gff"/>
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66 <output name="is_fasta" value="TEST_2/test_2.fna.is.fna"/>
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67 <output name="tpase_fasta" value="TEST_2/test_2.fna.orf.fna"/>
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68 <output name="tpase_amino" value="TEST_2/test_2.fna.orf.faa"/>
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69 <output name="logfile" value="TEST_2/test_2.log" lines_diff="50"/>
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70 </test>
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71 <test> <!-- TEST_3 without logfile and with csv output-->
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72 <param name="input_file" value="NC_012624.fna"/>
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73 <param name="remove_short_is" value="false"/>
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74 <param name="output_format" value="csv"/>
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75 <param name="log_activate" value="False"/>
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76 <output name="summary" value="TEST_3/test_3.fna.sum"/>
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77 <output name="is_results" value="TEST_3/test_3.fna.tsv"/>
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78 <output name="gff_file" value="TEST_3/test_3.fna.gff"/>
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79 <output name="is_fasta" value="TEST_3/test_3.fna.is.fna"/>
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80 <output name="tpase_fasta" value="TEST_3/test_3.fna.orf.fna"/>
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81 <output name="tpase_amino" value="TEST_3/test_3.fna.orf.faa"/>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85 **What it does**
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86 With
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87 ]]>
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88 </help>
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
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89 <expand macro="citations"/>
cecb2758ec26 planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
pimarin
parents:
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90 </tool>