Mercurial > repos > iuc > humann2_rna_dna_norm
view humann2_rna_dna_norm.xml @ 4:6893a2b1da17 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
author | iuc |
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date | Fri, 05 Feb 2021 18:25:13 +0000 |
parents | c8ef30c8451d |
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<tool id="humann2_rna_dna_norm" name="Normalize" version="@WRAPPER_VERSION@.1"> <description> combined meta'omic sequencing data</description> <macros> <import>humann2_macros.xml</import> </macros> <expand macro="stdio"/> <expand macro="requirements"/> <expand macro="version"/> <command detect_errors="exit_code"><![CDATA[ humann2_rna_dna_norm --input_dna '$input_dna' --input_rna '$input_rna' --output_basename 'results' --method '$method' #if $log.log_transform == 'yes' --log_transform --log_base $log.log_base #end if ]]></command> <inputs> <param argument="--input_dna" type="data" format="tsv,tabular,biom1" label="Original DNA output table"/> <param argument="--input_rna" type="data" format="tsv,tabular,biom1" label="Original RNA output table"/> <param argument="--method" type="select" label="Choice of smoothing method"> <option value="laplace">Laplace</option> <option value="witten_bell">Witten-Bell</option> </param> <conditional name="log"> <param argument="--log_transform" type="select" label="Report log-transformed relative expression values?"> <option value="yes">Yes</option> <option value="no">No</option> </param> <when value="yes"> <param argument="--log_base" type="integer" value="2" label="Base for log transformation"/> </when> <when value="no"/> </conditional> </inputs> <outputs> <data format="tsv" name="results-relative_expression" from_work_dir="results-relative_expression.tsv" label="${tool.name} on ${on_string}: normalized RNA"/> <data format="tsv" name="results-smoothed_dna" from_work_dir="results-smoothed_dna.tsv" label="${tool.name} on ${on_string}: smoothed DNA"/> <data format="tsv" name="results-smoothed_rna" from_work_dir="results-smoothed_rna.tsv" label="${tool.name} on ${on_string}: smoothed RNA"/> </outputs> <tests> <test> <param name="input_dna" value="rna_dna_norm-dna.txt"/> <param name="input_rna" value="rna_dna_norm-rna.txt"/> <param name="method" value="laplace"/> <conditional name="log"> <param name="log_transform" value="no"/> </conditional> <output name="results-relative_expression" md5="193000abf357cb14f70273ba6cd5f095"/> <output name="results-smoothed_dna" md5="3767aa13988a4dca40a07cb6970bcc60"/> <output name="results-smoothed_rna" md5="8b1bcb819c31ef0ba5ab4975582bfcf7"/> </test> <test> <param name="input_dna" value="rna_dna_norm-dna.txt"/> <param name="input_rna" value="rna_dna_norm-rna.txt"/> <param name="method" value="witten_bell"/> <conditional name="log"> <param name="log_transform" value="yes"/> <param name="log_base" value="2"/> </conditional> <output name="results-relative_expression" md5="3064e6377c074c6e6e9cf7fdfd466ec9"/> <output name="results-smoothed_dna" md5="3a1203c0986d79e9cb4ac0e3a4a89f4e"/> <output name="results-smoothed_rna" md5="1038b44e52b95a867dc6341b4dd91697"/> </test> </tests> <help><![CDATA[ @HELP_HEADER@ Given a DNA table and a RNA table, produce smoothed RNA and DNA values as well as relative expression values. "Smoothing" means substituting a small value in place of a zero or missing value. The default method used is "Laplace" (pseudocount) scaling, where the pseudocount is the sample-specific minimum non-zero value. (Witten-Bell smoothing is also implemented.) ]]></help> <expand macro="citations"/> </tool>