Mercurial > repos > rnateam > peakachu
changeset 3:600360da3986 draft default tip
"planemo upload for repository https://github.com/tbischler/PEAKachu commit 23fac1009bde8648151e533ce12c9f3d2f787a65-dirty"
| author | rnateam |
|---|---|
| date | Mon, 13 Sep 2021 17:20:30 +0000 |
| parents | 26304ccaca57 |
| children | |
| files | peakachu.xml |
| diffstat | 1 files changed, 9 insertions(+), 9 deletions(-) [+] |
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--- a/peakachu.xml Wed Jan 16 17:53:50 2019 -0500 +++ b/peakachu.xml Mon Sep 13 17:20:30 2021 +0000 @@ -1,9 +1,9 @@ -<tool id="peakachu" name="PEAKachu" version="0.1.0.2"> +<tool id="peakachu" name="PEAKachu" version="0.2.0+galaxy0" profile="20.01"> <description>Calls Peaks in CLIP data</description> <requirements> <requirement type="package" version="3.6">python</requirement> - <requirement type="package" version="3.4.1">r-base</requirement> - <requirement type="package" version="0.1.0">peakachu</requirement> + <requirement type="package" version="4.1.0">r-base</requirement> + <requirement type="package" version="0.2.0">peakachu</requirement> </requirements> <version_command> <![CDATA[ @@ -59,7 +59,7 @@ #end if --norm_method $mode.norm_method.norm_method_selector #if str($mode.norm_method.norm_method_selector) == 'manual': - --size_factors $size_factors + --size_factors '${mode.norm_method.size_factors}' #end if --mad_multiplier $mad_multiplier --fc_cutoff $fc_cutoff @@ -68,10 +68,10 @@ && if ls ./tmp_output/peak_tables/*.csv > /dev/null; then - cat ./tmp_output/peak_tables/*.csv | head -n 1 > peaks.tsv && + sed -n 1p ./tmp_output/peak_tables/*.csv > peaks.tsv && tail -n +2 -q ./tmp_output/peak_tables/*.csv >> peaks.tsv && mv peaks.tsv '$peak_tables' && - cat ./tmp_output/peak_annotations/*.gff | awk '/peak/ {print $0}' > peak_annotations.gff && + awk '/peak/ {print $0}' ./tmp_output/peak_annotations/*.gff > peak_annotations.gff && mv peak_annotations.gff '$peak_annotations' && mv ./tmp_output/plots/Initial*.png '$MA_plot'; else @@ -113,7 +113,7 @@ <param argument="--min_block_overlap" label="Minimum Block Overlap" help="Minimum fraction of the width of blocks for merging." type="float" value="0.5"/> <param argument="--min_max_block_expr" label="Minimum Block Expression" help="Minimum fraction of expression of blocks for merging." type="float" value="0.1"/> <conditional name="norm_method"> - <param name="norm_method_selector" type="select" label="Normalisation Method."> + <param name="norm_method_selector" type="select" label="Normalisation Method"> <option value="deseq" selected="True">DESeq2</option> <option value="manual">Manual</option> <option value="none">None</option> @@ -137,7 +137,7 @@ <option value="deseq">DESeq2</option> </param> <conditional name="norm_method"> - <param name="norm_method_selector" type="select" label="Normalisation Method."> + <param name="norm_method_selector" type="select" label="Normalisation Method"> <option value="tmm" selected="True">TMM</option> <option value="deseq">DESeq2</option> <option value="count">Count</option> @@ -149,7 +149,7 @@ <when value="count"/> <when value="none"/> <when value="manual"> - <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be seperated by SPACE"> + <param argument="--size_factors" label="Size Factors" type="text" help="Size factors have to be separated by SPACE"> <sanitizer> <valid initial="default"/> </sanitizer>