Mercurial > repos > rnateam > metilene
changeset 7:9ad744d0804b draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/metilene commit f332463404ef478e78d3ff4583b806dd68dfd3af-dirty
| author | rnateam |
|---|---|
| date | Thu, 18 Feb 2016 17:16:49 -0500 |
| parents | f9883968b113 |
| children | 48462181c628 |
| files | metilene.xml tool_dependencies.xml |
| diffstat | 2 files changed, 21 insertions(+), 12 deletions(-) [+] |
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--- a/metilene.xml Thu Dec 17 17:09:39 2015 -0500 +++ b/metilene.xml Thu Feb 18 17:16:49 2016 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="utf-8"?> -<tool id="metilene" name="metilene" version="0.2-4.0"> +<tool id="metilene" name="metilene" version="0.2-4.1"> <description> calling differentially methylated regions from bisulfite sequencing data </description> @@ -20,8 +20,8 @@ ## 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 && ## metilene main program @@ -30,11 +30,16 @@ -m $Options.opt_m -d $Options.opt_d -t 1 - -f 1 + #if $B: + -f 2 + -B "$B" + #else: + -f 1 + #end if -v $Options.opt_v metilene_g1_g2.input - >$output_bedlike - 2>/dev/null + > $output_bedlike + 2> /dev/null && ## postprocessing cut -f1-4 $output_bedlike > $output_bedgraph 2>/dev/null @@ -49,12 +54,16 @@ <!-- input bedgraph files 1 --> <param name="opt_in1" type="data" format="bed,bedgraph" multiple="true" label="Input group 1" - help="set of sorted bedgraph input profiles of group 1" /> + help="Set of sorted bedgraph/bed input profiles of group 1" /> <!-- input bedgraph files 2 --> <param name="opt_in2" type="data" format="bed,bedgraph" multiple="true" label="Input group 2" - help="set of sorted bedgraph input profiles of group 2" /> - + help="Set of sorted bedgraph/bed input profiles of group 2" /> + + <param argument="-B" type="data" format="bed" optional="True" + label="BED file containing regions of interest" + help="Regions that should be checked for differential methylation." /> + <!-- Advanced parameters (folded) --> <section name="Options" title="Advanced Options" expanded="False"> <param name="opt_M" type="integer" value="300"
--- a/tool_dependencies.xml Thu Dec 17 17:09:39 2015 -0500 +++ b/tool_dependencies.xml Thu Feb 18 17:16:49 2016 -0500 @@ -1,16 +1,16 @@ <?xml version="1.0"?> <tool_dependency> <package name="perl" version="5.18.1"> - <repository changeset_revision="2590d4683481" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="66db6ede3e0e" name="package_perl_5_18" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="R" version="3.2.1"> - <repository changeset_revision="c6ebd3a51334" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="9f31a291b305" name="package_r_3_2_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="bedtools" version="2.24"> <repository changeset_revision="e6f4a7398a47" name="package_bedtools_2_24" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="gnu_coreutils" version="8.22"> - <repository changeset_revision="1016a386a647" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="8b60cf3e0c07" name="package_gnu_coreutils_8_22" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="ggplot2" version="0.9.3"> <repository changeset_revision="ade406d47752" name="package_r_ggplot2_0_9_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />