Mercurial > repos > artbio > bigwig_to_wig
changeset 1:ac8ea1ca115d draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/bigwig_to_wig commit 85bdb086a4aa403465844a0b10399440b31b65a7
| author | artbio |
|---|---|
| date | Fri, 06 Oct 2023 00:19:35 +0000 |
| parents | ee2fbee916f7 |
| children | |
| files | bigwig_to_wig.sh bigwig_to_wig.xml macros.xml |
| diffstat | 3 files changed, 18 insertions(+), 22 deletions(-) [+] |
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--- a/bigwig_to_wig.sh Tue Sep 25 17:41:20 2018 -0400 +++ b/bigwig_to_wig.sh Fri Oct 06 00:19:35 2023 +0000 @@ -54,22 +54,22 @@ #for each chromsome while read line; do - - cur_chr=$(echo $line | cut --delimiter=" " -f1) - cur_length=$(echo $line | cut --delimiter=" " -f2) - + + cur_chr=$(echo $line | cut -d " " -f1) + cur_length=$(echo $line | cut -d " " -f2) + n_bins=$(echo "scale=0; (${cur_length}-${step_size})/${bin_size}" | bc) - + start=1 stop=$(echo "$n_bins * $bin_size" | bc) #write header line for each chromosome echo "fixedStep chrom=$cur_chr start=$start step=$step_size span=$step_size" - + #get densities along chr in n_bins with chosen bin_size and step_size (giving overlap in bins) nice bigWigSummary $bigwig_file $cur_chr $start $stop $n_bins | perl -pe 's/\t/\n/g' | perl -pe "s/n\/a/0/" #gives warning if no data in/for current chromosome - + done < $org_assembly_file #rm tmp
--- a/bigwig_to_wig.xml Tue Sep 25 17:41:20 2018 -0400 +++ b/bigwig_to_wig.xml Fri Oct 06 00:19:35 2023 +0000 @@ -1,4 +1,4 @@ -<tool id="bigwig_to_wig" name="BigWig to Wig" version="2.0.0"> +<tool id="bigwig_to_wig" name="BigWig to Wig" version="@VERSION@"> <description>converter</description> <macros> <import>macros.xml</import> @@ -8,7 +8,7 @@ <exit_code range="1:" level="fatal" description="Tool exception" /> </stdio> <command detect_errors="exit_code"><![CDATA[ - sh $__tool_directory__/bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output + bash $__tool_directory__/bigwig_to_wig.sh -f $input -b $bin_size -l $mylab > $output ]]></command> <inputs> <param name="input" format="bigwig" type="data" label="BigWig file to convert" /> @@ -23,13 +23,13 @@ <param name="input" value="1.bigwig" /> <param name="bin_size" value="500" /> <param name="mylab" value="wiggle_file" /> - <output name="output" file="1.wig" /> + <output name="output" file="1.wig" compare="sim_size" /> </test> <test> <param name="input" value="2.bigwig" /> <param name="bin_size" value="2000" /> <param name="mylab" value="wiggle_file" /> - <output name="output" file="2.wig" /> + <output name="output" file="2.wig" compare="sim_size" /> </test> </tests> <help><![CDATA[
--- a/macros.xml Tue Sep 25 17:41:20 2018 -0400 +++ b/macros.xml Fri Oct 06 00:19:35 2023 +0000 @@ -1,10 +1,11 @@ <macros> - <token name="@VERSION@">2.0.0</token> + <token name="@VERSION@">3+galaxy0</token> <macro name="requirements"> <requirements> - <requirement type="package" version="366">ucsc-bigwiginfo</requirement> - <requirement type="package" version="366">ucsc-bigwigsummary</requirement> - <requirement type="package" version="1.06">bc</requirement> + <requirement type="package" version="377">ucsc-bigwiginfo</requirement> + <requirement type="package" version="377">ucsc-bigwigsummary</requirement> + <requirement type="package" version="1.07.1">bc</requirement> + <requirement type="package" version="5.32.1">perl</requirement> </requirements> </macro> @@ -33,15 +34,10 @@ **Credits** -This tool is based on the script written by Jens Vilstrup Johansen and is an update of a Galaxy tool previously developed by nikos_. - -It uses bigWigInfo_ and bigWigSummary_. - -For support and bug reports contact Cedric Mendoza or Christophe Antoniewski or go to https://github.com/ARTbio/tools-artbio +This tool is based on the script written by Jens Vilstrup Johansen and is an update +of a Galaxy tool previously developed by nikos_. .. _nikos: https://toolshed.g2.bx.psu.edu/view/nikos/bigwig_to_wig/974af3268394 -.. _bigWigInfo: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigInfo -.. _bigWigSummary: https://github.com/adamlabadorf/ucsc_tools/blob/master/executables/bigWigSummary </token> </macros>