Mercurial > repos > jjohnson > samtools_split_by_chrom
changeset 0:a30dd3c77b30 draft
planemo upload commit 7491208ca0c917a053798a48c3e54c3e30e95d92
| author | jjohnson |
|---|---|
| date | Wed, 30 Nov 2016 16:46:40 -0500 |
| parents | |
| children | 6fb39843d37d |
| files | macros.xml samtools_split_by_chrom.xml tool_dependencies.xml |
| diffstat | 3 files changed, 138 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Nov 30 16:46:40 2016 -0500 @@ -0,0 +1,71 @@ +<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>echo $(samtools --version | head -n 1)", "$(samtools --version | grep -o -E "htslib.*?")</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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_split_by_chrom.xml Wed Nov 30 16:46:40 2016 -0500 @@ -0,0 +1,61 @@ +<tool id="samtools_split_by_chrom" name="Split BAM by Chromosome" version="2.0"> + <description>into collection</description> + <macros> + <import>macros.xml</import> + </macros> + <!-- <code file="samtools_slice_options.py"/> --> + <expand macro="requirements"></expand> + <expand macro="stdio"></expand> + <expand macro="version_command"></expand> + <command> +<![CDATA[ + mkdir -p outputs && + ln -s "${input_bam}" temp_input.bam && + ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai + #for $ref in str( $refs ).split(","): + && samtools view -@ \${GALAXY_SLOTS:-1} -bh inputs/temp_input.bam ${ref} | + samtools sort -O bam -T sorted -@ \${GALAXY_SLOTS:-1} -o "outputs/${input_bam.name}.${ref}.bam" - + #end for +]]> + </command> + <inputs> + <param name="input_bam" format="bam" label="Select BAM dataset to slice" type="data" /> + <param name="refs" type="select" optional="False" multiple="True" label="Select references (chromosomes and contigs) you would like to restrict bam to" help="Click and type in the box above to see options. You can select multiple entries. If "No options available" is displayed, you need to re-detect metadata on the input dataset. See help section below."> + <!-- The options tagset below extracts reference names from bam file metadata --> + <!-- This will not work with bed files with old style metadata. However this --> + <!-- Can be easily fixed by re-deceting metadata on a bam dataset by clicking --> + <!-- The pencil icon and settind datatype to "bam" --> + <!-- This change has been commited in the following pull request: --> + <!-- https://github.com/galaxyproject/galaxy/pull/107 --> + <options> + <filter type="data_meta" ref="input_bam" key="reference_names" /> + </options> + </param> + </inputs> + <outputs> + <collection name="output_collection" type='list' label="${input_bam.name} by chrom"> + <discover_datasets pattern="(?P<designation>.+)\.bam" directory="outputs" ext='bam'/> + </collection> + </outputs> + <tests> + <test> + <param ftype="bam" name="input_bam" value="bam-slice-input.bam" /> + <param name="refs" value="chrM" /> + <output file="bam-slice-test2.bam" ftype="bam" name="output_bam" /> + </test> + </tests> + <help> +<![CDATA[ + +**What it does** + +Creates a dataset collection of BAM files, one per selected chromosome. + +This tool is based on ``samtools view`` command. + +@no-chrom-options@ + +]]> + </help> + <expand macro="citations"></expand> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Nov 30 16:46:40 2016 -0500 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="1.2"> + <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>