| Previous changeset 0:57f3e32f809d (2015-04-21) Next changeset 2:135c85f4cfaf (2019-07-29) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_split commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40 |
|
modified:
macros.xml samtools_split.xml |
|
removed:
tool_dependencies.xml |
| b |
| diff -r 57f3e32f809d -r b7f7826ef1cd macros.xml --- a/macros.xml Tue Apr 21 17:44:16 2015 -0400 +++ b/macros.xml Tue May 09 11:18:30 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> |
| b |
| diff -r 57f3e32f809d -r b7f7826ef1cd samtools_split.xml --- a/samtools_split.xml Tue Apr 21 17:44:16 2015 -0400 +++ b/samtools_split.xml Tue May 09 11:18:30 2017 -0400 |
| [ |
| @@ -1,26 +1,26 @@ -<tool id="samtools_split" name="Split" version="1.1"> +<tool id="samtools_split" name="Split" version="@TOOL_VERSION@"> <description>BAM dataset on readgroups</description> <macros> <import>macros.xml</import> </macros> - <expand macro="requirements"></expand> - <expand macro="stdio"></expand> - <expand macro="version_command"></expand> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> <command><![CDATA[ samtools split -f 'Read_Group_%!.bam' #if $header: - -u "${output}":"${header}" + -u '${output}:${header}' #else: - -u "${output}" + -u '${output}' #end if "${input_bam}" - ]]></command> + ]]></command> <inputs> <param name="input_bam" type="data" format="bam" label="BAM file" /> - <param name="header" type="data" format="bam,sam" label="Replace header in output file" optional="True" /> + <param name="header" type="data" format="bam,sam" optional="True" label="Replace header in output file" /> </inputs> <outputs> - <data format="bam" name="output" label="${tool.name} on ${on_string}"> + <data name="output" format="bam" label="${tool.name} on ${on_string}"> <discover_datasets pattern="Read_Group_(?P<designation>.+)\.bam" ext="bam" visible="true" directory="" /> </data> </outputs> @@ -34,14 +34,12 @@ </output> </test> </tests> - <help> + <help><![CDATA[ **What it does** Splits BAM files on readgroups. -This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. - - </help> - <expand macro="citations"></expand> +This tool is based on ``samtools split`` command. It will generate multiple output datasets for each redagroup from the input dataset. + ]]></help> + <expand macro="citations"/> </tool> - |
| b |
| diff -r 57f3e32f809d -r b7f7826ef1cd tool_dependencies.xml --- a/tool_dependencies.xml Tue Apr 21 17:44:16 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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> |