Mercurial > repos > iuc > chewbbaca_allelecallevaluator
annotate AlleleCallEvaluator.xml @ 0:77a84fa4a02b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
author | iuc |
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date | Sat, 13 Apr 2024 16:08:53 +0000 |
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77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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1 <tool id="chewbbaca_allelecallevaluator" name="chewBBACA AlleleCallEvaluator" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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2 <description>Build an interactive report for allele calling results evaluation</description> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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3 <macros> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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4 <import>macros.xml</import> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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5 </macros> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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6 <expand macro="requirements" /> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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7 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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8 mkdir 'input' && |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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9 mkdir -p 'schema' && |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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10 #for $file in $input_file |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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11 ln -sf '$file' 'input/${file.element_identifier}.tsv' && |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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12 #end for |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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13 unzip '$input_schema' -d 'schema' && |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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14 chewBBACA.py AlleleCallEvaluator |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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15 #if $annotations: |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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16 -a '$annotations' |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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17 #end if |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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18 #if 'light' in $computation: |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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19 --light |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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20 #end if |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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21 #if 'no-pa' in $computation: |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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22 --no-pa |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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23 #end if |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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24 #if 'no-dm' in $computation: |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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25 --no-dm |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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26 #end if |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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27 #if 'no-tree' in $computation: |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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28 --no-tree |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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29 #end if |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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30 #if 'cg-alignment' in $computation: |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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31 --cg-alignment |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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32 #end if |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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33 -i 'input' -g 'schema/schema_seed/' -o '${html_file.files_path}' |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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34 && cp '${html_file.files_path}'/*\.html output.html |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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35 |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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36 ]]></command> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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37 <inputs> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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38 <param name="input_file" type="data_collection" collection_type="list" label="AlleleCall Results" format="tabular"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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39 <param name="input_schema" format="zip" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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40 <section name="advanced" title="Advanced options"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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41 <param argument="--annotations" type="data" format="tabular" label="Annotation file" help="File created by the UniprotFinder module" optional="true" /> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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42 <param name="computation" type="select" multiple="true" optional="true" display="checkboxes" label="Computation method"> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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43 <option value="light">Do not compute the presence-absence matrix, the distance matrix, and the Neighbor-Joining tree. --light</option> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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44 <option value="no-pa">Do not compute the presence-absence matrix. --no-pa</option> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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45 <option value="no-dm">Do not compute the distance matrix. --no-dm</option> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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46 <option value="no-tree">Do not compute the Neighbor-Joining tree. --no-tree</option> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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47 <option value="cg-alignment">Compute the MSA of the core genome loci, even if `--no-tree` is provided. --cg-alignment</option> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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48 </param> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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49 </section> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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50 </inputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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51 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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52 <data format="html" name="html_file" from_work_dir="output.html" label="${tool.name} on ${on_string}: Webpage" /> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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53 </outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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54 <tests> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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55 <test expect_exit_code="0"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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56 <param name="input_file"> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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57 <collection type="list"> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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58 <element name="cds_coordinates" value="cds_coordinates.tsv" ftype="tabular"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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59 <element name="loci_summary_stats" value="loci_summary_stats.tsv" ftype="tabular"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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60 <element name="results_alleles" value="results_alleles.tsv" ftype="tabular"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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61 <element name="results_statistics" value="results_statistics.tsv" ftype="tabular"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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62 </collection> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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63 </param> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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64 <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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65 <output name="html_file" file="allelecallevaluator_report.html" ftype="html" compare="diff"> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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66 </output> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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67 </test> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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68 <test expect_exit_code="0"> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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69 <param name="input_file"> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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70 <collection type="list"> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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71 <element name="cds_coordinates" value="cds_coordinates.tsv" ftype="tabular"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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72 <element name="loci_summary_stats" value="loci_summary_stats.tsv" ftype="tabular"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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73 <element name="results_alleles" value="results_alleles.tsv" ftype="tabular"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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74 <element name="results_statistics" value="results_statistics.tsv" ftype="tabular"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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75 </collection> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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76 </param> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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77 <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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78 <param name="annotations" value="schema_seed_annotations.tsv"/> |
77a84fa4a02b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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79 <output name="html_file" file="allelecallevaluator_report_annotate.html" ftype="html"> |
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80 <assert_contents> |
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81 <has_text_matching expression=""annotations""/> |
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82 <has_text_matching expression=""Uniprot_Name""/> |
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83 </assert_contents> |
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84 </output> |
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85 </test> |
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86 </tests> |
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87 <help> |
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88 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results. |
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89 |
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90 The AlleleCallEvaluator module allows users to generate an interactive HTML report to evaluate allele calling results generated by the AlleleCall module. The report provides summary statistics to evaluate results per sample and per locus (with the possibility to provide a TSV file with loci annotations to include on a table). The report includes components to display a heatmap representing the loci presence-absence matrix, a heatmap representing the distance matrix based on allelic differences and a Neighbor-Joining (NJ) tree based on the MSA of the core genome loci. |
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91 |
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92 .. class:: warningmark |
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93 |
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94 **Warning** |
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95 |
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96 The JS bundle is necessary to visualize the HTML report. Do not move or delete this file. |
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97 |
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98 </help> |
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99 <expand macro="citations" /> |
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100 </tool> |