Mercurial > repos > devteam > print_reads
changeset 1:a8b94864fe35 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/gatk/print_reads commit a1517c9d22029095120643bbe2c8fa53754dd2b7
| author | devteam |
|---|---|
| date | Wed, 11 Nov 2015 12:44:29 -0500 |
| parents | e768f4851646 |
| children | |
| files | print_reads.xml tool_dependencies.xml |
| diffstat | 2 files changed, 4 insertions(+), 13 deletions(-) [+] |
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--- a/print_reads.xml Tue Apr 01 10:48:38 2014 -0400 +++ b/print_reads.xml Wed Nov 11 12:44:29 2015 -0500 @@ -1,4 +1,4 @@ -<tool id="gatk_print_reads" name="Print Reads" version="0.0.1"> +<tool id="gatk_print_reads" name="Print Reads" version="0.0.2"> <description>from BAM files</description> <requirements> <requirement type="package" version="1.4">gatk</requirement> @@ -73,7 +73,7 @@ <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" help="-platform,--platform &lt;platform&gt;" /> <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" help="-readGroup,--readGroup &lt;readGroup&gt;" /> <repeat name="sample_file_repeat" title="File containing a list of samples to include" help="-sf,--sample_file &lt;sample_file&gt;"> - <param name="input_sample_file" type="data" format="text" label="Sample file" /> + <param name="input_sample_file" type="data" format="txt" label="Sample file" /> </repeat> <repeat name="sample_name_repeat" title="Sample name to be included in the analysis" help="-sn,--sample_name &lt;sample_name&gt;"> <param name="sample_name" type="text" label="Sample name" /> @@ -86,15 +86,6 @@ <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (BAM)" /> <data format="txt" name="output_log" label="${tool.name} on ${on_string} (log)" /> </outputs> - <param name="number" type="integer" value="-1" label="Print the first n reads from the file, discarding the rest" /> - <param name="platform" type="text" value="" label="Exclude all reads with this platform from the output" /> - <param name="read_group" type="text" value="" label="Exclude all reads with this read group from the output" /> - <repeat name="sample_file_repeat" title="File containing a list of samples to include"> - <param name="input_sample_file" type="data" format="text" label="Sample file" /> - </repeat> - <repeat name="sample_name_repeat" title="Sample name to be included in the analysis"> - <param name="sample_name" type="text" label="Sample name" /> - </repeat> <tests> <test> <param name="reference_source_selector" value="history" />
--- a/tool_dependencies.xml Tue Apr 01 10:48:38 2014 -0400 +++ b/tool_dependencies.xml Wed Nov 11 12:44:29 2015 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="gatk" version="1.4"> - <repository changeset_revision="ec95ec570854" name="package_gatk_1_4" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="ec95ec570854" name="package_gatk_1_4" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency>