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view add_group_rank.xml @ 2:caba07f41453 draft default tip
"planemo upload for repository https://github.com/secimTools/SECIMTools/tree/main/galaxy commit 498abad641099412df56f04ff6e144e4193bbc34-dirty"
author | malex |
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date | Thu, 10 Jun 2021 15:41:17 +0000 |
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<tool id="secimtools_rank_group_wide" name="Ranked wide file" version="@WRAPPER_VERSION@"> <description>Generate a wide format file with ranked columns from an input wide file.</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ add_group_rank.py --wide $wide --design $design --out $out #if $ngroup: --ngroup $ngroup #end if --uniqID $uniqID ]]></command> <inputs> <param name="wide" type="data" format="tabular" label="Wide Dataset" help="Input dataset in wide format and tab separated. If file is not tab separated see TIP below."/> <param name="design" type="data" format="tabular" label="Design File" help="Design file tab separated. Note you need a 'sampleID' column. If not tab separated see TIP below."/> <param name="uniqID" type="text" size="30" value="rowID" label="Unique Feature ID" help="Name of the column in your Wide Dataset that has unique Feature IDs."/> <param name="ngroup" type="integer" size="30" value="" optional="true" label="number of groups for each feature being ranked" help="number of bins/groups for each feature being ranked. If there is no input, the default behavir is ranking each column."/> </inputs> <outputs> <data format="tabular" name="out" label="${tool.name} on ${on_string}: Results Table"/> </outputs> <tests> <test> <param name="wide" value="ST000006_data.tsv"/> <param name="design" value="ST000006_design.tsv"/> <param name="uniqID" value="Retention_Index" /> <param name="ngroup" value="100" /> <output name="out" file="ST000006_add_group_rank_output_wide.tsv" /> </test> </tests> <help><![CDATA[ @TIP_AND_WARNING@ **Tool Description** The tool is used to generate a wide format file with each column being ranked in the input wide format dataset. -------------------------------------------------------------------------------- **Input** - Two input datasets are required. An example of input wide file is like: +---------+---------+---------+---------+-----+ | Feature | sample1 | sample2 | sample3 | ... | +=========+=========+=========+=========+=====+ | one | 10.2 | 20 | 10 | ... | +---------+---------+---------+---------+-----+ | two | 5.1 | 22 | 30 | ... | +---------+---------+---------+---------+-----+ | three | 30.5 | 27 | 2 | ... | +---------+---------+---------+---------+-----+ | four | 32.9 | 17 | 8 | ... | +---------+---------+---------+---------+-----+ | ... | ... | ... | ... | ... | +---------+---------+---------+---------+-----+ -------------------------------------------------------------------------------- **Output** The user will get a output file from the tool: - a wide format file with each column being ranked. The output wide file for the example above will be like: +---------+---------+---------+---------+-----+ | Feature | sample1 | sample2 | sample3 | ... | +=========+=========+=========+=========+=====+ | one | 2 | 2 | 3 | ... | +---------+---------+---------+---------+-----+ | two | 1 | 3 | 4 | ... | +---------+---------+---------+---------+-----+ | three | 3 | 4 | 1 | ... | +---------+---------+---------+---------+-----+ | four | 4 | 1 | 2 | ... | +---------+---------+---------+---------+-----+ | ... | ... | ... | ... | ... | +---------+---------+---------+---------+-----+ ]]></help> <expand macro="citations"/> </tool>