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condor.xml
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condor.xml
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<tool id="condor" name="condor" version="0.2">
<description>ConDor: A workflow to detect convergent evolution</description>
<requirements>
<requirement type="package" version="1.8.0">java</requirement>
<requirement type="package">apptainer</requirement>
</requirements>
<stdio>
<exit_code range="1:" level="fatal"/>
</stdio>
<command>
<![CDATA[
bash $__tool_directory__/nextflow run
-c $__tool_directory__/nextflow.config -profile pasteurgalaxy
$__tool_directory__/condor.nf
#if $model == "best":
--model ${model}
#else:
--model ${model}${invariant}${rates}
#end if
--align ${seq}
--tree ${tree}
--outgroup ${outgroup}
--phenotype ${phenotype}
--resdir results
--min_seq ${minconvseqs}
--min_eem ${mineems}
--nb_simu 10000
--matrices $__tool_directory__/assets/protein_model.txt
--freqmode ${freqmode}
--branches ${branches}
--correction holm
--alpha ${alpha}
--bayes ${bayes};
]]>
</command>
<inputs>
<param name="seq" format="fasta" type="data" label="Alignment file" help="Fasta format"/>
<param name="tree" format="nhx" type="data" label="Tree file" help="Newick format"/>
<param name="outgroup" format="txt" type="data" label="Outgroup file" help="Txt format, one taxon per line"/>
<param name="phenotype" format="txt" type="data" label="Phenotype file" help="Txt format, taxon with convergent phenotype, one taxon per line"/>
<param name="model" type="select" label="Evolutionary model">
<option value="best" selected="true">Best (IQ-TREE Model finder)</option>
<option value="POISSON" selected="false">POISSON</option>
<option value="DAYHOFF" selected="false">DAYHOFF</option>
<option value="DCMUT" selected="false">DCMUT</option>
<option value="JTT" selected="false">JTT</option>
<option value="MTREV" selected="false">MTREV</option>
<option value="WAG" selected="false">WAG</option>
<option value="RTREV" selected="false">RTREV</option>
<option value="CPREV" selected="false">CPREV</option>
<option value="VT" selected="false">VT</option>
<option value="BLOSUM62" selected="false">BLOSUM62</option>
<option value="MTMAM" selected="false">MTMAM</option>
<option value="LG" selected="false">LG</option>
<option value="MTART" selected="false">MTART</option>
<option value="MTZOA" selected="false">MTZOA</option>
<option value="PMB" selected="false">PMB</option>
<option value="HIVB" selected="false">HIVB</option>
<option value="HIVW" selected="false">HIVW</option>
<option value="JTTDCMUT" selected="false">JTTDCMUT</option>
<option value="FLU" selected="false">FLU</option>
<option value="MTMET" selected="false">MTMET</option>
<option value="MTVER" selected="false">MTVER</option>
<option value="MTINV" selected="false">MTINV</option>
<option value="Q_PFAM" selected="false">Q_PFAM</option>
<option value="Q_PFAM_GB" selected="false">Q_PFAM_GB</option>
<option value="Q_LG" selected="false">Q_LG</option>
<option value="Q_BIRD" selected="false">Q_BIRD</option>
<option value="Q_INSECT" selected="false">Q_INSECT</option>
<option value="Q_MAMMAL" selected="false">Q_MAMMAL</option>
<option value="Q_PLANT" selected="false">Q_PLANT</option>
<option value="Q_YEAST" selected="false">Q_YEAST</option>
<option value="FLAVI" selected="false">FLAVI</option>
</param>
<param name="invariant" type="select" label="Invariant sites">
<option value="" selected="true">empty</option>
<option value="+I" selected="false">+I</option>
</param>
<param name="rates" type="select" label="Rate heterogeneity">
<option value="" selected="true">No rate heteorogeneity</option>
<option value="+G4" selected="false">+G4</option>
<option value="+G5" selected="false">+G5</option>
<option value="+G6" selected="false">+G6</option>
<option value="+G8" selected="false">+G8</option>
<option value="+G10" selected="false">+G10</option>
<option value="+R3" selected="false">+R3</option>
<option value="+R4" selected="false">+R4</option>
<option value="+R6" selected="false">+R6</option>
<option value="+R8" selected="false">+R8</option>
<option value="+R10" selected="false">+R10</option>
</param>
<param name="freqmode" type="select" label="Equilibrium frequencies">
<option value="Fmodel" selected="true">Frequencies of the model</option>
<option value="FO" selected="false">Frequencies optimized by maximum likelihood</option>
</param>
<param name="minconvseqs" type="select" label="Minimum number of convergent sequences (>=)">
<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="7">7</option>
<option value="8">8</option>
<option value="9">9</option>
<option value="10" selected="true">10</option>
<option value="11">11</option>
<option value="12">12</option>
<option value="14">14</option>
<option value="16">16</option>
<option value="18">18</option>
<option value="20">20</option>
</param>
<param name="mineems" type="select" label="Minimum number of emergence event of a mutation (>=)">
<option value="2">2</option>
<option value="3" selected="true">3</option>
<option value="4">4</option>
<option value="5">5</option>
<option value="6">6</option>
<option value="7">7</option>
<option value="8">8</option>
<option value="9">9</option>
<option value="10">10</option>
<option value="11">11</option>
<option value="12">12</option>
<option value="14">14</option>
<option value="16">16</option>
<option value="18">18</option>
<option value="20">20</option>
</param>
<param name="branches" type="select" label="CONDOR run mode">
<option value="condor" selected="true">condor</option>
<option value="emergence">emergence</option>
<option value="correlation">correlation</option>
</param>
<param name="alpha" type="select" label="P.value emergence">
<option value="0.01">0.01</option>
<option value="0.015">0.015</option>
<option value="0.025">0.025</option>
<option value="0.05">0.05</option>
<option value="0.1" selected="true">0.1</option>
<option value="0.15">0.15</option>
<option value="0.2">0.2</option>
</param>
<param name="bayes" type="select" label="log BF correlation">
<option value="2">2</option>
<option value="4">4</option>
<option value="5">5</option>
<option value="7">7</option>
<option value="10" selected="true">10</option>
<option value="12">12</option>
<option value="15">15</option>
<option value="20">20</option>
</param>
</inputs>
<outputs>
<data name="tested_results" format="tsv" label="Tested metrics" from_work_dir="results/tested_results.tsv" />
<data name="significant_results" format="tsv" label="Detected metrics" from_work_dir="results/significant_results.tsv" />
</outputs>
<help>
</help>
<citations>
</citations>
</tool>