Mercurial > repos > devteam > samtool_filter2
changeset 3:c31a37f6d48a draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/samtool_filter2 commit d02925461fc5d6188099a60c1996c671a0bde828
| author | devteam |
|---|---|
| date | Thu, 17 Mar 2016 11:39:47 -0400 |
| parents | 886b73f04847 |
| children | d3292b4a0c78 |
| files | samtool_filter2.xml tool_dependencies.xml |
| diffstat | 2 files changed, 7 insertions(+), 6 deletions(-) [+] |
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--- a/samtool_filter2.xml Fri Oct 09 17:24:03 2015 -0400 +++ b/samtool_filter2.xml Thu Mar 17 11:39:47 2016 -0400 @@ -1,7 +1,7 @@ -<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.1"> +<tool id="samtool_filter2" name="Filter SAM or BAM, output SAM or BAM" version="1.1.2"> <description>files on FLAG MAPQ RG LN or by region</description> <requirements> - <requirement type="package" version="0.1.18">samtools</requirement> + <requirement type="package" version="1.2">samtools</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -17,7 +17,7 @@ #set $input = 'input.sam' ln -s "$input1" $input && #end if -samtools view -o "$output1" $header +samtools view $possibly_select_inverse "$output1" $header #if $input1.datatype.file_ext == 'sam': -S @@ -115,6 +115,7 @@ <param name="read_group" type="text" value="" label="Select alignments from Read Group" help="(-r) Requires headers in the input SAM or BAM, otherwise no alignments will be output"/> <param name="bed_file" type="data" format="bed" optional="true" label="Output alignments overlapping the regions in the BED FILE" help="(-L)"/> + <param name="possibly_select_inverse" checked="false" label="Use inverse selection" type="boolean" truevalue="-U" falsevalue="-o" help="Select the opposite of the listed chromosomes" /> <param name="regions" type="text" value="" label="Select regions (only used when the input is in BAM format)" help="region should be presented in one of the following formats: `chr1', `chr2:1,000' and `chr3:1000-2,000'"/> <param name="outputtype" type="select" label="Select the output format">
--- a/tool_dependencies.xml Fri Oct 09 17:24:03 2015 -0400 +++ b/tool_dependencies.xml Thu Mar 17 11:39:47 2016 -0400 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="samtools" version="0.1.18"> - <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> </tool_dependency>