Mercurial > repos > devteam > samtools_sort
changeset 6:191cec7b989b draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:56:00 -0400 |
| parents | 346239545aa0 |
| children | 4ab677d8c0de |
| files | macros.xml samtools_sort.xml test-data/1_sort_read_names.bam tool_dependencies.xml |
| diffstat | 4 files changed, 89 insertions(+), 23 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 13 12:56:00 2015 -0400 @@ -0,0 +1,70 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.2">samtools</requirement> + <yield/> + </requirements> + </xml> + <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},} + </citation> + <citation type="doi">10.1093/bioinformatics/btp352</citation> + <citation type="doi">10.1093/bioinformatics/btr076</citation> + <citation type="doi">10.1093/bioinformatics/btr509</citation> + <citation type="bibtex"> + @misc{Danecek_et_al, + Author={Danecek, P., Schiffels, S., Durbin, R.}, + title={Multiallelic calling model in bcftools (-m)}, + url = {http://samtools.github.io/bcftools/call-m.pdf},} + </citation> + <citation type="bibtex"> + @misc{Durbin_VCQC, + Author={Durbin, R.}, + title={Segregation based metric for variant call QC}, + url = {http://samtools.github.io/bcftools/rd-SegBias.pdf},} + </citation> + <citation type="bibtex"> + @misc{Li_SamMath, + Author={Li, H.}, + title={Mathematical Notes on SAMtools Algorithms}, + url = {http://www.broadinstitute.org/gatk/media/docs/Samtools.pdf},} + </citation> + <citation type="bibtex"> + @misc{SamTools_github, + title={SAMTools GitHub page}, + url = {https://github.com/samtools/samtools},} + </citation> + </citations> + </xml> + <xml name="version_command"> + <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> + </xml> + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + </xml> + <token name="@no-chrom-options@"> +----- + +.. class:: warningmark + +**No options available? How to re-detect metadata** + +If you see a "No options available" within the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop down, you need to re-detect metadata for the dataset you are trying to process. To do this follow these steps: + +1. Click on the **pencil** icon adjacent to the dataset in the history +2. A new menu will appear in the center pane of the interface +3. Click **Datatype** tab +4. Set **New Type** to **BAM** +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 Thu Oct 16 12:42:20 2014 -0400 +++ b/samtools_sort.xml Tue Oct 13 12:56:00 2015 -0400 @@ -1,18 +1,17 @@ -<tool id="samtools_sort" name="sort" version="1.0.3"> - <requirements> - <requirement type="package" version="1.1">samtools</requirement> - </requirements> - <description>a BAM file</description> - <version_command>samtools --version | head -n 1 | awk '{ print $2 }'</version_command> - <command>samtools sort $sort_mode "${input1}" -o "${output1}" -O bam -T dataset</command> - <stdio> - <exit_code range="1:" level="fatal" description="Error" /> - </stdio> +<tool id="samtools_sort" name="Sort" version="2.0"> + <description>BAM dataset</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> <inputs> <param name="input1" type="data" format="bam" label="BAM File" /> <param name="sort_mode" type="select" label="Sort by "> <option value="" selected="True">Chromosomal coordinates</option> - <option value="-n">Read names</option> + <option value="-n">Read names (-n)</option> </param> </inputs> <outputs> @@ -23,22 +22,19 @@ <param name="input1" value="1.bam" ftype="bam" /> <output name="output1" file="1_sort.bam" ftype="bam" sort="True"/> </test> + <test> + <param name="input1" value="1.bam" ftype="bam" /> + <param name="sort_mode" value="-n"/> + <output name="output1" file="1_sort_read_names.bam" ftype="bam" sort="True"/> + </test> </tests> <help> **What it does** -This tool uses the SAMTools_ toolkit to sort alignments by leftmost coordinates or read names. - -.. _SAMTools: http://samtools.sourceforge.net/samtools.shtml - ------- +This tool uses ``samtools sort`` command to sort BAM datasets in coordinate or read name order. -**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> + <expand macro="citations"></expand> </tool>
--- a/tool_dependencies.xml Thu Oct 16 12:42:20 2014 -0400 +++ b/tool_dependencies.xml Tue Oct 13 12:56:00 2015 -0400 @@ -1,6 +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 name="samtools" version="1.2"> + <repository changeset_revision="192f00129358" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>