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comparison parse_mykrobe_predict.xml @ 1:0ac12c344bfa draft default tip

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planemo upload for repository https://github.com/katholt/sonneityping commit 4d048786a4cf9ecb045fa3263084f98105c15557
author iuc
date Tue, 12 Mar 2024 15:37:17 +0000
parents db4fe7172114
children
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0:db4fe7172114 1:0ac12c344bfa
1 <tool id="sonneityping" name="parse mykrobe predict" version="@TOOL_VERSION@" profile="20.05"> 1 <tool id="sonneityping" name="parse mykrobe predict" version="@TOOL_VERSION@" profile="20.05">
2 <description>for Shigella sonnei and tabulate results into a single tab-delimited file</description> 2 <description>for Shigella sonnei and tabulate results into a single tab-delimited file</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <xrefs>
7 <xref type="bio.tools">sonneityping</xref>
8 </xrefs>
6 <expand macro="requirements"/> 9 <expand macro="requirements"/>
7 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
8 parse_mykrobe_predict --jsons 11 parse_mykrobe_predict --jsons
9 12
10 #for $i in $json 13 #for $i in $json
29 <data format="tabular" label="parsed output" name="parsed_output" from_work_dir="results_predictResults.tsv" /> 32 <data format="tabular" label="parsed output" name="parsed_output" from_work_dir="results_predictResults.tsv" />
30 </outputs> 33 </outputs>
31 <tests> 34 <tests>
32 <test> 35 <test>
33 <param name="json" ftype="json" value="SRR6114360.json"/> 36 <param name="json" ftype="json" value="SRR6114360.json"/>
34 <param name="optional.alleles" ftype="txt" value="alleles.txt" /> 37 <param name="alleles" ftype="txt" value="alleles.txt" />
35 <output name="parsed_output"> 38 <output name="parsed_output">
36 <assert_contents> 39 <assert_contents>
37 <has_text text="3.7.30.4" /> 40 <has_text text="3.7.30.4" />
38 <has_text text="S. sonnei" /> 41 <has_text text="S. sonnei" />
39 </assert_contents> 42 </assert_contents>