Mercurial > repos > rnateam > metilene
diff metilene.xml @ 4:cd253831a014 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit 9bc3c9b613d106098a78e16534897c88a3738c07
| author | rnateam |
|---|---|
| date | Sat, 24 Dec 2016 18:03:49 -0500 |
| parents | df838db0b597 |
| children | 37abd09a0ae6 |
line wrap: on
line diff
--- a/metilene.xml Wed Jul 13 07:41:40 2016 -0400 +++ b/metilene.xml Sat Dec 24 18:03:49 2016 -0500 @@ -1,17 +1,12 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="metilene" name="metilene" version="0.2.6.0"> +<tool id="metilene" name="metilene" version="0.2.6.1"> <description> calling differentially methylated regions from bisulfite sequencing data </description> <requirements> <requirement type="package" version="0.2.6">metilene</requirement> - <requirement type="package" version="5.18.1">perl</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> + <requirement type="package" version="8.25">coreutils</requirement> </requirements> <stdio> <exit_code range=":-1"/> @@ -22,8 +17,8 @@ ## preprocessing ## generate metilene_g1_g2.input from multiple bedgraph files metilene_input.pl - --in1 "$opt_in1" - --in2 "$opt_in2" + --in1 '$opt_in1' + --in2 '$opt_in2' >/dev/null ##2>/dev/null && @@ -48,7 +43,7 @@ -v $Options.opt_v metilene_g1_g2.input - > $output_bedlike + > '$output_bedlike' ##2> /dev/null && ## postprocessing @@ -56,7 +51,7 @@ && ## write to job directory metilene_output.pl - -q $output_bedlike + -q '$output_bedlike' -p 0.05 -o ./metilene ##>/dev/null