Mercurial > repos > yhoogstrate > samtools_view_header
changeset 0:73429bd06e71 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Wed, 11 Jun 2014 08:21:14 -0400 |
| parents | |
| children | e233adca8052 |
| files | samtools_view_header.xml tool_dependencies.xml |
| diffstat | 2 files changed, 58 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_view_header.xml Wed Jun 11 08:21:14 2014 -0400 @@ -0,0 +1,48 @@ +<?xml version="1.0" encoding="UTF-8"?> +<tool id="samtools_view_header" name="Samtools view header"> + <description>Show only the header of a BAM or SAM file using samtools.</description> + <requirements> + <requirement type="package" version="5.9">ncurses</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <command> + samtools + view + -H + #if $alignment.dataset.ext.lower() == "sam" + -S + #end if + $alignment > $header 2> stderr.txt ; + + cat stderr.txt + </command> + + <inputs> + <param format="sam,bam" name="alignment" type="data" label="Alignments in BAM or SAM format" help="The set of aligned reads." /> + </inputs> + + <outputs> + <data format="tabular" name="header" label="${tool.name} on ${alignment.name}" /> + </outputs> + + <help> +**samtools view -H ** + +**Input formats** + +**Installation** + + +**License** + +* samtools: .... + +**Contact** + +The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project: +http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch + +More tools by the Translational Research IT (TraIT) project can be found in the following repository: +http://toolshed.dtls.nl/ +</help> +</tool> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jun 11 08:21:14 2014 -0400 @@ -0,0 +1,10 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncurses" version="5.9"> + <repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> + + <package name="samtools" version="0.1.19"> + <repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> \ No newline at end of file