Mercurial > repos > iuc > chewbbaca_createschema
annotate CreateSchema.xml @ 0:4e61ec4fd5f5 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 16:09:20 +0000 |
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children | 6a8df4d75f3a |
rev | line source |
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0
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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1 <tool id="chewbbaca_createschema" name="chewBBACA CreateSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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2 <description>Create a gene-by-gene schema</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> |
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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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5 </macros> |
4e61ec4fd5f5
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" /> |
4e61ec4fd5f5
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' && |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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9 #for $file in $input_file |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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10 ln -sf '$file' 'input/${file.element_identifier}' && |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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11 #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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12 chewBBACA.py CreateSchema |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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13 #if $training_file: |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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14 --ptf '$training_file' |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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15 #end if |
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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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16 $cds_input |
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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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17 @COMMON_INPUT@ |
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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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18 --pm $prodigal_mode |
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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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19 -i 'input' -o 'output' && |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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20 cd 'output/' && |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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21 zip -r schema_seed.zip 'schema_seed' |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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22 ]]></command> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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23 <inputs> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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24 <param format="fasta" name="input_file" type="data" multiple="True" label="Genome assemblies in FASTA format"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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25 <section name="advanced" title="Advanced options"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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26 <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" /> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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27 <param argument="--cds-input" type="boolean" truevalue="--cds-input" falsevalue="" checked="false" label="CDS input" optional="true"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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28 <param argument="--minimum-length" type="integer" min="0" value="201" label="Minimum sequence length value"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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29 <expand macro="common_param" /> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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30 <param argument="--prodigal-mode" type="select" label="Prodigal Mode" help=""single" for finished genomes, reasonable quality draft genomes and big viruses. "meta" for metagenomes, low quality draft genomes, small viruses, and small plasmids"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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31 <option value="single" selected="true"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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32 single |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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33 </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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34 <option value="meta"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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35 meta |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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36 </option> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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37 </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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38 </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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39 <section name="output" title="Output options"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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40 <param name="show_cds_invalid" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output invalid CDS file?"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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41 <param name="show_cds_coord" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Output CDS coordinates File?"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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42 </section> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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43 </inputs> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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44 <outputs> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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45 <data format="zip" name="schema" from_work_dir="output/schema_seed.zip" label="${tool.name} on ${on_string}: Schema files"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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46 <data format="txt" name="txt_file" from_work_dir="output/invalid_cds.txt" label="${tool.name} on ${on_string}: Invalid CDS"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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47 <filter>output['show_cds_invalid']</filter> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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48 </data> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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49 <data format="tabular" name="tsv_file" from_work_dir="output/cds_coordinates.tsv" label="${tool.name} on ${on_string}: CDS coordinates"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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50 <filter>output['show_cds_coord']</filter> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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51 </data> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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52 </outputs> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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53 <tests> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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54 <test expect_num_outputs="1"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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55 <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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56 <output name="schema"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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57 <assert_contents> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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58 <has_archive_member path="schema_seed/.*\.fasta" n="204"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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59 <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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60 <has_archive_member path="schema_seed/\.schema_config"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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61 </assert_contents> |
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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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62 </output> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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63 </test> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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64 <test expect_num_outputs="1"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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65 <param name="input_file" value="GCA_000007265.1_ASM726v1_genomic.fna"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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66 <param name="training_file" value="Streptococcus_agalactiae.trn"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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67 <output name="schema"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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68 <assert_contents> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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69 <has_archive_member path="schema_seed/.*\.fasta" n="198"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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70 <has_archive_member path="schema_seed/short/.*\.fasta" n="99"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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71 <has_archive_member path="schema_seed/\.schema_config"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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72 </assert_contents> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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73 </output> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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74 </test> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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75 <test expect_num_outputs="1"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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76 <param name="input_file" value="CDS_Str_agalactiae.fasta"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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77 <param name="cds_input" value="true"/> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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78 <output name="schema"> |
4e61ec4fd5f5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
iuc
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79 <assert_contents> |
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80 <has_archive_member path="schema_seed/CDS-Str-agalactiae-protein1.fasta"/> |
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81 </assert_contents> |
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82 </output> |
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83 </test> |
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84 </tests> |
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85 <help> |
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86 |
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87 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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88 |
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89 A Schema is a pre-defined set of loci that is used in MLST analyses. Traditional MLST schemas relied in 7 loci that were internal fragments of housekeeping genes and each locus was defined by its amplification by a pair of primers yielding a fragment of a defined size. |
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90 |
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91 In genomic analyses, schemas are a set of loci that are: |
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92 |
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93 - Present in the majority of strains for core genome (cg) MLST schemas, typically a threshold of presence in 95% of the strains is used in schema creation. The assumption is that in each strain up to 5% of loci may not be identified due to sequencing coverage problems, assembly problems or other issues related to the use of draft genome assemblies. |
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94 - Present in at least one of the analyzed strains in the schema creation for pan genome/whole genome (pg/wg) MLST schemas. |
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95 - Present in less than 95% of the strains for accessory genome (ag) MLST schemas. |
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96 |
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97 .. class:: infomark |
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98 |
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99 **Note** |
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100 |
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101 These definitions are always operational in nature, in the sense that the analyses are performed on a limited number of strains representing part of the biological diversity of a given species or genus and are always dependent on the definition of thresholds. |
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102 |
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103 .. class:: infomark |
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104 |
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105 **Important** |
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106 |
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107 The use of a prodigal training file for schema creation is highly recommended. |
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108 |
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109 .. class:: infomark |
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110 |
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111 **Important** |
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112 |
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113 If you provide the **--cds-input** parameter, chewBBACA assumes that the input FASTA files contain coding sequences and skips the gene prediction step with Prodigal. To avoid issues related with the format of the sequence headers, chewBBACA renames the sequence headers based on the unique basename prefix determined for each input file and on the order of the coding sequences (e.g.: coding sequences inside a file named GCF_000007125.1_ASM712v1_cds_from_genomic.fna are renamed to GCF_000007125-protein1, GCF_000007125-protein2, …, GCF_000007125-proteinN). |
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114 |
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115 </help> |
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116 <expand macro="citations" /> |
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117 </tool> |