Mercurial > repos > iuc > chewbbaca_nsstats
diff NSStats.xml @ 0:ebbbb3265867 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 16:09:46 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NSStats.xml Sat Apr 13 16:09:46 2024 +0000 @@ -0,0 +1,50 @@ +<tool id="chewbbaca_nsstats" name="chewBBACA NSStats" version="@CHEW_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> + <description>Retrieve basic information about the species and schemas in Chewie-NS</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + chewBBACA.py NSStats + -m $mode + #if $species_id != "" + --sp $species_id + #end if + #if $schema_id != "" + --sc $schema_id + #end if + > 'NSStats.txt' + ]]></command> + <inputs> + <param argument="--mode" type="select" label="Mode" optional="false"> + <option value="species">species</option> + <option value="schemas">schemas</option> + </param> + <param argument="--species-id" type="select" label="Species ID" value="" optional="true"> + <expand macro="species_id"/> + </param> + <!-- Currently,the schema id can only be set to 1. Maybe in the next versions other values possible --> + <param argument="--schema-id" type="integer" min="1" value="" label="Schema ID" optional="true"/> + </inputs> + <outputs> + <data format="txt" name="NSStats" from_work_dir="NSStats.txt" label="${tool.name}"/> + </outputs> + <tests> + <test expect_exit_code="0"> + <param name="mode" value="species" /> + <output name="NSStats"> + <assert_contents> + <has_text_matching expression="Streptococcus pyogenes\s+1\s+1\s+3044\s+398511"/> + <has_text_matching expression="Clostridium neonatale\s+16\s+1\s+2350\s+13115"/> + </assert_contents> + </output> + </test> + </tests> + <help> +chewBBACA is a software suite for the creation and evaluation of core genome and whole genome MultiLocus Sequence Typing (cg/wgMLST) schemas and results. + +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. + + </help> + <expand macro="citations" /> +</tool> \ No newline at end of file