Mercurial > repos > iuc > chewbbaca_nsstats

comparison NSStats.xml @ 0:97a24534a0c0 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chewbbaca commit 8bb518e20d68623904232ae28bb8a51ec05c1c4a
author iuc
date Wed, 25 Sep 2024 14:12:51 +0000
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:97a24534a0c0
1 <tool id="chewbbaca_nsstats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Retrieve basic information about the species and schemas in Chewie-NS</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 chewBBACA.py NSStats
9 -m $mode
10 #if $species_id != ""
11 --sp $species_id
12 #end if
13 #if $schema_id != ""
14 --sc $schema_id
15 #end if
16 > 'NSStats.txt'
17 ]]></command>
18 <inputs>
19 <param argument="--mode" type="select" label="Mode" optional="false">
20 <option value="species">species</option>
21 <option value="schemas">schemas</option>
22 </param>
23 <param argument="--species-id" type="select" label="Species ID" value="" optional="true">
24 <expand macro="species_id"/>
25 </param>
26 <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible -->
27 <param argument="--schema-id" type="integer" min="1" value="" label="Schema ID" optional="true"/>
28 </inputs>
29 <outputs>
30 <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name}"/>
31 </outputs>
32 <tests>
33 <test expect_exit_code="0">
34 <param name="mode" value="species" />
35 <output name="NSStats">
36 <assert_contents>
37 <has_text_matching expression="Streptococcus pyogenes\s+1\s+1\s+3044\s+398511"/>
38 <has_text_matching expression="Clostridium neonatale\s+16\s+1\s+2350\s+13115"/>
39 </assert_contents>
40 </output>
41 </test>
42 </tests>
43 <help>
44 chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results.
45
46 The NSStats module enables the retrieval of information from the Chewie-NS server. Its main objective is to provide information about the list of species and schemas in Chewie-NS, so that users can quickly identify a schema of interest and download it.
47
48 </help>
49 <expand macro="citations" />
50 </tool>