Mercurial > repos > rnateam > metilene
changeset 3:df838db0b597 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit 0dc67759bcbdf5a8a285ded9ba751340d741fe63
| author | rnateam |
|---|---|
| date | Wed, 13 Jul 2016 07:41:40 -0400 |
| parents | 3dbc8ee72d39 |
| children | cd253831a014 |
| files | metilene.xml tool_dependencies.xml |
| diffstat | 2 files changed, 30 insertions(+), 9 deletions(-) [+] |
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--- a/metilene.xml Tue Feb 23 07:28:12 2016 -0500 +++ b/metilene.xml Wed Jul 13 07:41:40 2016 -0400 @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="metilene" name="metilene" version="0.2-4.1"> +<tool id="metilene" name="metilene" version="0.2.6.0"> <description> calling differentially methylated regions from bisulfite sequencing data </description> <requirements> - <requirement type="package" version="0.2-4">metilene</requirement> + <requirement type="package" version="0.2.6">metilene</requirement> <requirement type="package" version="5.18.1">perl</requirement> - <requirement type="package" version="0.9.3">r_ggplot2</requirement> + <!--requirement type="package" version="3.2.1">R</requirement--> + <!--requirement type="package" version="0.9.3">r_ggplot2</requirement--> + + <requirement type="package" version="2.0.0">r-ggplot2</requirement> <requirement type="package" version="2.24">bedtools</requirement> <requirement type="package" version="8.22">gnu_coreutils</requirement> </requirements> @@ -14,31 +17,39 @@ <exit_code range=":-1"/> <exit_code range="1:" /> </stdio> - <version_command>echo "0.2-4"</version_command> + <version_command>echo "0.2.6"</version_command> <command><![CDATA[ ## preprocessing ## generate metilene_g1_g2.input from multiple bedgraph files metilene_input.pl --in1 "$opt_in1" --in2 "$opt_in2" - >/dev/null 2>/dev/null + >/dev/null + ##2>/dev/null && ## metilene main program metilene -M $Options.opt_M -m $Options.opt_m -d $Options.opt_d - -t 1 + -t \${GALAXY_SLOTS:-4} #if $B: -f 2 -B "$B" #else: -f 1 #end if + #if $Options.Y: + -Y $Options.Y + #end if + #if $Options.X: + -X $Options.X + #end if + -v $Options.opt_v metilene_g1_g2.input > $output_bedlike - 2> /dev/null + ##2> /dev/null && ## postprocessing cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null @@ -47,7 +58,9 @@ metilene_output.pl -q $output_bedlike -p 0.05 - -o ./metilene >/dev/null 2>/dev/null + -o ./metilene + ##>/dev/null + ##2>/dev/null ]]></command> <inputs> <!-- input bedgraph files 1 --> @@ -73,6 +86,14 @@ label="The minimum # of CpGs in a DMR" help="-m, --mincpgs"/> + <param argument="X" type="integer" value="" optional="True" + label="Specify how many replicates must contain data for a certain CpG position in group 1" + help="to estimate missing ones"/> + + <param argument="Y" type="integer" value="" optional="True" + label="Specify how many replicates must contain data for a certain CpG position in group 2" + help="to estimate missing ones"/> + <param name="opt_d" type="float" value="0.1" label="The minimum mean methylation difference for calling DMRs" help="-d, --minMethDiff"/>
--- a/tool_dependencies.xml Tue Feb 23 07:28:12 2016 -0500 +++ b/tool_dependencies.xml Wed Jul 13 07:41:40 2016 -0400 @@ -1,7 +1,7 @@ <?xml version="1.0"?> <tool_dependency> <package name="perl" version="5.18.1"> - <repository changeset_revision="d905bb415eca" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="bedtools" version="2.24"> <repository changeset_revision="39b86c1e267d" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />