Mercurial > repos > iuc > chewbbaca_prepexternalschema

comparison PrepExternalSchema.xml @ 2:0b73dd40d83f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 501c1cb91f4b91ec93e6df6e555323bbe8e2b703
author iuc
date Fri, 07 Jun 2024 14:27:17 +0000
parents 6f7cfce9494d
children
comparison
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1:7035fc8b4ae3 2:0b73dd40d83f
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[ 7 <command detect_errors="exit_code"><![CDATA[
8 mkdir 'schema' &&
9 unzip '$input_schema' -d 'schema' && 8 unzip '$input_schema' -d 'schema' &&
10 chewBBACA.py PrepExternalSchema 9 chewBBACA.py PrepExternalSchema
11 #if $training_file: 10 #if $training_file:
12 --ptf '$training_file' 11 --ptf '$training_file'
13 #end if 12 #end if
14 #if $genes_list: 13 #if $genes_list:
15 --gl '$genes_list' 14 --gl '$genes_list'
16 #end if 15 #end if
17 @COMMON_INPUT@ 16 @COMMON_INPUT@
18 $size_filter 17 $size_filter
19 -g 'schema/schema_seed/' -o 'schema_seed' && 18 -g 'schema/' -o 'schema_seed' &&
20 zip -r PExternalschema_seed.zip 'schema_seed' 19 zip -r PExternalschema_seed.zip 'schema_seed'
21 ]]></command> 20 ]]></command>
22 <inputs> 21 <inputs>
23 <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and a folder named 'short' that contains the FASTA files with the loci representative alleles."/> 22 <param format="zip" name="input_schema" type="data" label="Schema Files in zip format" help="The schema directory contains the loci FASTA files and the schema must contain one FASTA file per gene/locus."/>
24 <section name="advanced" title="Advanced options"> 23 <section name="advanced" title="Advanced options">
25 <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" /> 24 <param argument="--training-file" type="data" format="binary" label="Prodigal training file" optional="true" />
26 <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" /> 25 <param argument="--genes-list" type="data" format="txt" label="Gene list" optional="true" />
27 <param argument="--minimum-length" type="integer" min="0" value="0" label="Minimum sequence length value"/> 26 <param argument="--minimum-length" type="integer" min="0" value="0" label="Minimum sequence length value"/>
28 <expand macro="common_param" /> 27 <expand macro="common_param" />
32 <outputs> 31 <outputs>
33 <data format="zip" name="schema" from_work_dir="PExternalschema_seed.zip" label="${tool.name} on ${on_string}: PrepExternal Schema files"/> 32 <data format="zip" name="schema" from_work_dir="PExternalschema_seed.zip" label="${tool.name} on ${on_string}: PrepExternal Schema files"/>
34 </outputs> 33 </outputs>
35 <tests> 34 <tests>
36 <test expect_num_outputs="1"> 35 <test expect_num_outputs="1">
37 <param name="input_schema" value="GCA_000007265.1_ASM726v1_schema_seed.zip"/> 36 <param name="input_schema" value="PrepExternal_test.zip"/>
38 <param name="size_filter" value="false"/> 37 <param name="size_filter" value="false"/>
39 <output name="schema"> 38 <output name="schema">
40 <assert_contents> 39 <assert_contents>
41 <has_archive_member path="schema_seed/.*\.fasta" n="204"/> 40 <has_archive_member path="schema_seed/.*\.fasta" n="204"/>
42 <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/> 41 <has_archive_member path="schema_seed/short/.*\.fasta" n="102"/>