Mercurial > repos > rnateam > metilene
changeset 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 |
| files | metilene.xml tool_dependencies.xml |
| diffstat | 2 files changed, 6 insertions(+), 58 deletions(-) [+] |
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--- 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
--- a/tool_dependencies.xml Wed Jul 13 07:41:40 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,47 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="perl" version="5.18.1"> - <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" /> - </package> - <package name="gnu_coreutils" version="8.22"> - <repository changeset_revision="ac64dfe4b1fb" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="ggplot2" version="0.9.3"> - <repository changeset_revision="07de191649b4" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="metilene" version="0.2-4"> - <install version="1.0"> - <actions> - <action sha256sum="7430b4c2af4f43d389ad690dfe42c9ce7a63b2bff4ff0ac59afc0f1ec7e600f2" type="download_by_url"> - https://depot.galaxyproject.org/software/metilene/metilene_0.2-4_src_all.tar.gz - </action> - <action type="shell_command">make</action> - <!-- move binary and scripts to installation bin directory --> - <action type="move_file"> - <source>metilene</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>metilene_input.pl</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>metilene_output.pl</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - <action type="move_file"> - <source>metilene_output.R</source> - <destination>$INSTALL_DIR/bin</destination> - </action> - - <action type="set_environment"> - <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> - </action> - </actions> - </install> - <readme>Metilene is precompiled for Linux</readme> - </package> -</tool_dependency>