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Alexander OSTROVSKY authored and Alexander OSTROVSKY committed Nov 15, 2024
1 parent 31f692d commit 857f362
Showing 1 changed file with 34 additions and 43 deletions.
77 changes: 34 additions & 43 deletions tools/checkm2/checkm2.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,31 +6,31 @@
<token name="@IDX_DATA_TABLE@">checkm2_db_versioned</token>
</macros>
<xrefs>
<xref type="bio.tools">dada2</xref>
<xref type="bio.tools">checkm2</xref>
</xrefs>
<requirements>
<requirement type="package" version="@TOOL_VERSION@">checkm2</requirement>
</requirements>
<command detect_errors="exit_code"><![CDATA[
mkdir input_dir &&
#for $i, $file in enumerate($input):
cp $file input_dir/${file.element_identifier}.dat &&
#set $cleaned = re.sub('[^\s\w\-\\.]', '_', str($file.element_identifier))
ln -s $file input_dir/${cleaned}.dat &&
#end for
checkm2 predict
--input input_dir
$model
$genes
#if $ttable_manual.set_ttable == "yes":
--ttable $ttable_manual.ttable
#if $ttable:
--ttable $ttable
#end if
-x .dat
--threads "\${GALAXY_SLOTS:-1}"
--database_path $database.fields.path
--database_path '$database.fields.path'
--output-directory output
]]></command>
<inputs>
<param name="input" type="data" format="fasta" label="Input MAG/SAG datasets" multiple="true"/>

<param name="database" type="select" label="Select reference genome" help="Checkm2 Diamond database">
<options from_data_table="@IDX_DATA_TABLE@">
<filter type="sort_by" column="2"/>
Expand All @@ -45,43 +45,34 @@
<option value="--specific">Force the use of the specific quality prediction model (neural network)</option>
<option value="--allmodels">Output quality prediction for both models for each genome.</option>
</param>
<conditional name="ttable_manual">
<param name="set_ttable" type="select" help="If not chosen, tool will automatically determine either 11 or 4" label="Manually set specific progidal translation table?">
<option value='no'>No</option>
<option value="yes">Yes</option>
</param>
<when value="no"/>
<when value="yes">
<!-- It's not all numbers and there's a check internally if it's in a specific list, so it had to be spelled out -->
<param argument="ttable" type="select" label="Prodigal table">
<option value="1">1</option>
<option value="2">2</option>
<option value="3">3</option>
<option value="4">4</option>
<option value="5">5</option>
<option value="6">6</option>
<option value="9">9</option>
<option value="10">10</option>
<option value="11">11</option>
<option value="12">12</option>
<option value="13">13</option>
<option value="14">14</option>
<option value="16">16</option>
<option value="21">21</option>
<option value="22">22</option>
<option value="23">23</option>
<option value="24">24</option>
<option value="25">25</option>
<option value="26">26</option>
<option value="27">27</option>
<option value="28">28</option>
<option value="29">29</option>
<option value="30">30</option>
<option value="31">31</option>
<option value="33">33</option>
</param>
</when>
</conditional>
<!-- It's not all numbers and there's a check internally if it's in a specific list, so it had to be spelled out -->
<param argument="ttable" type="select" label="Prodigal table" optional="true">
<option value="1">1. The Standard Code</option>
<option value="2">2. The Vertebrate Mitochondrial Code</option>
<option value="3">3. The Yeast Mitochondrial Code</option>
<option value="4">4. The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option>
<option value="5">5. The Invertebrate Mitochondrial Code</option>
<option value="6">6. The Ciliate, Dasycladacean and Hexamita Nuclear Code</option>
<option value="9">9. The Echinoderm and Flatworm Mitochondrial Code</option>
<option value="10">10. The Euplotid Nuclear Code</option>
<option value="11">11. The Bacterial, Archaeal and Plant Plastid Code</option>
<option value="12">12. The Alternative Yeast Nuclear Code</option>
<option value="13">13. The Ascidian Mitochondrial Code</option>
<option value="14">14. The Alternative Flatworm Mitochondrial Code</option>
<option value="16">16. Chlorophycean Mitochondrial Code</option>
<option value="21">21. Trematode Mitochondrial Code</option>
<option value="22">22. Scenedesmus obliquus Mitochondrial Code</option>
<option value="23">23. Thraustochytrium Mitochondrial Code</option>
<option value="24">24. Rhabdopleuridae Mitochondrial Code</option>
<option value="25">25. Candidate Division SR1 and Gracilibacteria Code</option>
<option value="26">26. Pachysolen tannophilus Nuclear Code</option>
<option value="27">27. Karyorelict Nuclear Code</option>
<option value="28">28. Condylostoma Nuclear Code</option>
<option value="29">29. Mesodinium Nuclear Code</option>
<option value="30">30. Peritrich Nuclear Code</option>
<option value="31">31. Blastocrithidia Nuclear Code</option>
<option value="33">33. Cephalodiscidae Mitochondrial UAA-Tyr Code</option>
</param>
</inputs>
<outputs>
<data name="quality" label="${tool.name} on ${on_string}: Quality report" format="tabular" from_work_dir="output/quality_report.tsv"/>
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