Mercurial > repos > devteam > samtools_bedcov
changeset 0:6ffa7e68dc1f draft
Uploaded initial tool definition.
| author | devteam |
|---|---|
| date | Mon, 27 Oct 2014 12:42:42 -0400 |
| parents | |
| children | 4f7acd7af617 |
| files | samtools_bedcov.xml test-data/eboVir3.1.bed test-data/eboVir3.2.bam test-data/eboVir3.2.bed test-data/eboVir3.bam test-data/samtools_bedcov_out1.tab test-data/samtools_bedcov_out2.tab tool_dependencies.xml |
| diffstat | 8 files changed, 80 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_bedcov.xml Mon Oct 27 12:42:42 2014 -0400 @@ -0,0 +1,62 @@ +<tool id="samtools_bedcov" name="Calculate read depth" version="1.0.0"> + <description>on BAM files</description> + <requirements> + <requirement type="package" version="1.1">samtools</requirement> + </requirements> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + <command><![CDATA[ + for bamfile in + #for dataset in $input_bams: + "${dataset}" + #end for + ; do + if [ ! -f \$bamfile.bai ] ; then + ln -s \$bamfile && samtools index `basename \$bamfile` ; + else + ln -s \$bamfile && ln -s \$bamfile.bai ; + fi ; + done ; + samtools bedcov "${input_bed}" + #for dataset in $input_bams: + `basename "${dataset}"` + #end for + > "${output}" + ]]></command> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <inputs> + <param name="input_bed" type="data" format="bed" label="BED file" /> + <param name="input_bams" type="data" format="bam" label="BAM file" multiple="true" /> + </inputs> + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> + </outputs> + <tests> + <test> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + <param name="input_bams" value="eboVir3.bam" ftype="bam" /> + <output name="output" file="samtools_bedcov_out1.tab" /> + </test> + <test> + <param name="input_bed" value="eboVir3.1.bed" ftype="bed" /> + <param name="input_bams" value="eboVir3.bam,eboVir3.2.bam" ftype="bam" /> + <output name="output" file="samtools_bedcov_out2.tab" /> + </test> + </tests> + <help> +**What it does** + +This tool runs the ``samtools bedcov`` command in the SAMtools toolkit. + +Show read depth per BED region. + +**Citation** + +For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ + + +If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* + </help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eboVir3.1.bed Mon Oct 27 12:42:42 2014 -0400 @@ -0,0 +1,3 @@ +eboVir3 500 1500 +eboVir3 1500 2000 +eboVir3 1500 3000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eboVir3.2.bed Mon Oct 27 12:42:42 2014 -0400 @@ -0,0 +1,3 @@ +eboVir3 500 1500 +eboVir3 1500 2000 +eboVir3 1500 3000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_bedcov_out1.tab Mon Oct 27 12:42:42 2014 -0400 @@ -0,0 +1,3 @@ +eboVir3 500 1500 7919 +eboVir3 1500 2000 3009 +eboVir3 1500 3000 9986
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_bedcov_out2.tab Mon Oct 27 12:42:42 2014 -0400 @@ -0,0 +1,3 @@ +eboVir3 500 1500 7919 2094 +eboVir3 1500 2000 3009 1064 +eboVir3 1500 3000 9986 3455
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Oct 27 12:42:42 2014 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.1"> + <repository changeset_revision="c01b111a243b" name="package_samtools_1_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>