Mercurial > repos > iuc > prepexternalschema

annotate PrepExternalSchema.xml @ 0:0dbb7224d23c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
author iuc
date Sat, 13 Apr 2024 16:08:39 +0000
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0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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1 <tool id="prepexternalschema" name="chewBBACA PrepExternalSchema" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Adapt an external schema to be used with chewBBACA</description>
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3 <macros>
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iuc
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4 <import>macros.xml</import>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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5 </macros>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir 'schema' &&
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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9 unzip '$input_schema' -d 'schema' &&
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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10 chewBBACA.py PrepExternalSchema
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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11 #if $training_file:
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12 --ptf '$training_file'
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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13 #end if
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14 #if $genes_list:
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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15 --gl '$genes_list'
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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16 #end if
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17 @COMMON_INPUT@
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18 $size_filter
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19 -g 'schema/schema_seed/' -o 'schema_seed' &&
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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20 zip -r PExternalschema_seed.zip 'schema_seed'
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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21 ]]></command>
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22 <inputs>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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23 <param format="zip" name="input_schema" 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."/>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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24 <section name="advanced" title="Advanced options">
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25 <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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26 <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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27 <param argument="--minimum-length" type="integer" min="0" value="0" label="Minimum sequence length value"/>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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28 <expand macro="common_param" />
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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29 <param argument="--size-filter" type="boolean" truevalue="--size-filter" falsevalue="" checked="false" label="Size filter" help="Apply the minimum length and size threshold values to filter out alleles during schema adaptation" />
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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30 </section>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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31 </inputs>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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32 <outputs>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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33 <data format="zip" name="schema" from_work_dir="PExternalschema_seed.zip" label="${tool.name} on ${on_string}: PrepExternal Schema files"/>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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34 </outputs>
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35 <tests>
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36 <test expect_num_outputs="1">
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37 <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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38 <param name="size_filter" value="false"/>
0dbb7224d23c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8722918e903ffa4229e0297555731f1172f736c6
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39 <output name="schema">
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40 <assert_contents>
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41 <has_archive_member path="schema_seed/.*\.fasta" n="204"/>
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42 <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/>
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43 <has_archive_member path="schema_seed/\.schema_config"/>
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44 </assert_contents>
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45 </output>
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46 </test>
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47 </tests>
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48 <help>
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49
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50 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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51
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52 The PrepExternalSchema module enables the adaptation of external schemas so that it is possible to use those schemas with chewBBACA.
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53
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54 </help>
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55 <expand macro="citations" />
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56 </tool>