Mercurial > repos > bgruening > deeptools
changeset 70:a4bbac56f046 draft
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit f720d773e34ad90d14d7cae77c1a0bb5d126102c-dirty
| author | bgruening |
|---|---|
| date | Fri, 18 Sep 2015 06:17:07 -0400 |
| parents | 0eb2441d1fcf |
| children | 106cd88dc9da |
| files | deepTools_macros.xml tool_dependencies.xml |
| diffstat | 2 files changed, 9 insertions(+), 19 deletions(-) [+] |
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--- a/deepTools_macros.xml Sun May 31 08:35:35 2015 -0400 +++ b/deepTools_macros.xml Fri Sep 18 06:17:07 2015 -0400 @@ -192,14 +192,9 @@ </xml> <xml name="multiple_input_bams"> - <repeat name="input_files" title="BAM files" min="2"> - <param name="bamfile" type="data" format="bam" - label="Bam file" - help="The BAM file must be sorted."/> - <param name="label" type="text" size="30" optional="true" value="" - label="Label" - help="Label to use in the output. If not given the dataset name will be used instead."/> - </repeat> + <param name="bamfiles" type="data" format="bam" + label="Bam file" multiple="true" + help="The BAM file must be sorted."/> </xml> <xml name="multiple_input_bigwigs"> @@ -224,20 +219,15 @@ #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) #set files=[] #set labels=[] - #for $i in $input_files: + #for $i in $bamfiles: #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) #set $temp_input_path = $temp_input_handle.name #silent $temp_input_handle.close() - #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) - #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) + #silent os.system("ln -s %s %s.bam" % (str($i), $temp_input_path)) + #silent os.system("ln -s %s %s.bam.bai" % (str($i.metadata.bam_index), $temp_input_path)) #silent $files.append('%s.bam' % $temp_input_path) - ##set $files += [str($i.bamfile)] - #if str($i.label.value) != "": - #set $labels += ["\"%s\"" % ($i.label.value)] - #else - #set $labels += ["\"%s\"" % ($i.bamfile.name)] - #end if + #silent $labels.append("\"%s\"" % ($i.name)) #end for </token>
--- a/tool_dependencies.xml Sun May 31 08:35:35 2015 -0400 +++ b/tool_dependencies.xml Fri Sep 18 06:17:07 2015 -0400 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="python" version="2.7"> - <repository changeset_revision="fb14ceede7bc" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="94e61bd56e40" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="deepTools" version="1.5.10"> - <repository changeset_revision="c4cdf0686bce" name="package_python_2_7_deeptools_1_5_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="093b1359d8d2" name="package_python_2_7_deeptools_1_5_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>