Mercurial > repos > devteam > samtools_sort
changeset 1:cab3f8d35989 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_sort commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author | iuc |
---|---|
date | Tue, 09 May 2017 11:18:12 -0400 |
parents | a430da4f04cd |
children | f56bdb93ae58 |
files | macros.xml samtools_sort.xml tool_dependencies.xml |
diffstat | 3 files changed, 21 insertions(+), 23 deletions(-) [+] |
line wrap: on
line diff
--- a/macros.xml Tue Apr 21 17:41:18 2015 -0400 +++ b/macros.xml Tue May 09 11:18:12 2017 -0400 @@ -1,16 +1,17 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.2">samtools</requirement> + <requirement type="package" version="1.3.1">samtools</requirement> <yield/> </requirements> </xml> + <token name="@TOOL_VERSION@">1.3.1</token> <xml name="citations"> <citations> <citation type="bibtex"> @misc{SAM_def, title={Definition of SAM/BAM format}, - url = {https://samtools.github.io/hts-specs/SAMv1.pdf},} + url = {https://samtools.github.io/hts-specs/},} </citation> <citation type="doi">10.1093/bioinformatics/btp352</citation> <citation type="doi">10.1093/bioinformatics/btr076</citation> @@ -41,7 +42,7 @@ </citations> </xml> <xml name="version_command"> - <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -64,7 +65,5 @@ 5. Click **Save** The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. - </token> - </macros>
--- a/samtools_sort.xml Tue Apr 21 17:41:18 2015 -0400 +++ b/samtools_sort.xml Tue May 09 11:18:12 2017 -0400 @@ -1,12 +1,20 @@ -<tool id="samtools_sort" name="Sort" version="2.0"> - <description>BAM dataset</description> +<tool id="samtools_sort" name="Sort" version="2.0.1"> + <description>order of storing aligned sequences</description> <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio"></expand> - <expand macro="version_command"></expand> - <command>samtools sort $sort_mode -@ \${GALAXY_SLOTS:-1} -o "${output1}" -O bam -T dataset "${input1}"</command> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + samtools sort + $sort_mode + -@ \${GALAXY_SLOTS:-1} + -o '${output1}' + -O bam + -T dataset + '${input1}' + ]]></command> <inputs> <param name="input1" type="data" format="bam" label="BAM File" /> <param name="sort_mode" type="select" label="Sort by "> @@ -29,12 +37,9 @@ </test> </tests> <help> - **What it does** This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order. - - </help> - <expand macro="citations"></expand> + <expand macro="citations"/> </tool>
--- a/tool_dependencies.xml Tue Apr 21 17:41:18 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="samtools" version="1.2"> - <repository changeset_revision="6eea04363026" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>