Mercurial > repos > prog > isa2w4m
diff isa2w4m.xml @ 1:1facef3ba64a draft default tip
"planemo upload commit 9683b1655539660ed1e983783a72a5c3016238bd-dirty"
author | prog |
---|---|
date | Wed, 27 Apr 2022 16:38:56 +0000 |
parents | 1883d5274962 |
children |
line wrap: on
line diff
--- a/isa2w4m.xml Wed Jan 08 09:56:00 2020 -0500 +++ b/isa2w4m.xml Wed Apr 27 16:38:56 2022 +0000 @@ -1,10 +1,11 @@ <!-- vi: se fdm=marker : --> -<tool id="isa2w4m" name="ISA to W4M" version="1.1.1"> +<tool id="isa2w4m" name="ISA to W4M" version="1.1.3"> <description>Convert ISA data type into W4M format</description> <requirements> - <requirement type="package" version="0.10.3">isatools</requirement> + <requirement type="package" version="1.2.5">pandas</requirement> + <requirement type="package" version="0.12.2">isatools</requirement> </requirements> <!-- Command {{{1 --> @@ -13,29 +14,33 @@ ## @@@BEGIN_CHEETAH@@@ $__tool_directory__/isa2w4m.py - -i "$isa.extra_files_path" - -s "$w4m_sample_metadata" - -v "$w4m_variable_metadata" - -m "$w4m_data_matrix" + -i '$isa.extra_files_path' + -s '$w4m_sample_metadata' + -v '$w4m_variable_metadata' + -m '$w4m_data_matrix' ## Choose study to output #if $study: - -n "$study" + -n '$study' #end if ## Choose assay to output #if $assay: - -f "$assay" + -f '$assay' #end if ## Filtering #if $sample_na_filtering: - -S "$sample_na_filtering" + -S '$sample_na_filtering' #end if #if $variable_na_filtering: - -V "$variable_na_filtering" + -V '$variable_na_filtering' #end if + ## Redirect stderr to stdout otherwise Galaxy thinks the tool fails if + ## it sees just one character on stderr. + 2>&1 + ## @@@END_CHEETAH@@@ ]]></command> @@ -65,6 +70,12 @@ <output name="w4m_sample_metadata" file="MTBLS30-w4m-sample-metadata.tsv"/> <output name="w4m_data_matrix" file="MTBLS30-w4m-sample-variable-matrix.tsv"/> </test> + <test> + <param name="isa" value="MTBLS174.zip" ftype="isa-tab"/> + <output name="w4m_variable_metadata" file="MTBLS174-w4m-variable-metadata.tsv"/> + <output name="w4m_sample_metadata" file="MTBLS174-w4m-sample-metadata.tsv"/> + <output name="w4m_data_matrix" file="MTBLS174-w4m-sample-variable-matrix.tsv"/> + </test> </tests> <!-- Help {{{1 -->