Mercurial > repos > devteam > samtools_slice_bam
changeset 3:a4a10c7924d1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_slice_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
| author | iuc |
|---|---|
| date | Tue, 09 May 2017 11:17:27 -0400 |
| parents | 2b474ebbfc7d |
| children | 344fc91e1bfd |
| files | macros.xml samtools_slice_bam.xml tool_dependencies.xml |
| diffstat | 3 files changed, 39 insertions(+), 55 deletions(-) [+] |
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--- a/macros.xml Tue Apr 21 17:37:49 2015 -0400 +++ b/macros.xml Tue May 09 11:17:27 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 $2 }'</version_command> + <version_command><![CDATA[samtools 2>&1 | grep Version]]></version_command> </xml> <xml name="stdio"> <stdio> @@ -64,7 +65,5 @@ 5. Click **Save** The medatada will be re-detected and you will be able to see the list of reference sequences in the "**Select references (chromosomes and contigs) you would like to restrict bam to**" drop-down. - </token> - </macros>
--- a/samtools_slice_bam.xml Tue Apr 21 17:37:49 2015 -0400 +++ b/samtools_slice_bam.xml Tue May 09 11:17:27 2017 -0400 @@ -1,43 +1,40 @@ -<tool id="samtools_slice_bam" name="Slice" version="2.0"> - <description>BAM by genomic regions</description> - <macros> - <import>macros.xml</import> - </macros> - <!-- <code file="samtools_slice_options.py"/> --> - <expand macro="requirements"></expand> - <expand macro="stdio"></expand> - <expand macro="version_command"></expand> - <command> -<![CDATA[ - ln -s "${input_bam}" temp_input.bam && - ln -s "${input_bam.metadata.bam_index}" temp_input.bam.bai && +<tool id="samtools_slice_bam" name="Slice" version="2.0.1"> + <description>BAM by genomic regions</description> + <macros> + <import>macros.xml</import> + </macros> + + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + + <command><![CDATA[ + ln -s '${input_bam}' temp_input.bam && + ln -s '${input_bam.metadata.bam_index}' temp_input.bam.bai && #if str($slice_method.slice_method_selector) == "bed": - samtools view -@ \${GALAXY_SLOTS:-1} -b -L "${input_interval}" -o unsorted_output.bam temp_input.bam && - #elif str($slice_method.slice_method_selector) == "chr": - samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam ${ ' '.join( map( lambda x:'"%s"' % ( x ), str( $slice_method.refs ).split(",") ) ) } && - #elif str($slice_method.slice_method_selector) == "man": - samtools view -@ \${GALAXY_SLOTS:-1} -b -o unsorted_output.bam temp_input.bam #for $region in $slice_method.regions: "${region.chrom}:${region.start}-${region.end}" #end for - && - #end if - samtools sort -O bam -T sorted -@ \${GALAXY_SLOTS:-1} -o "${output_bam}" unsorted_output.bam -]]> - </command> + samtools sort + -O bam + -T sorted + -@ \${GALAXY_SLOTS:-1} + -o '${output_bam}' + unsorted_output.bam + ]]></command> <inputs> - <param name="input_bam" format="bam" label="Select BAM dataset to slice" type="data" /> + <param name="input_bam" type="data" format="bam" label="Select BAM dataset to slice" /> <conditional name="slice_method"> <param name="slice_method_selector" type="select" label="How do you want to slice your dataset?"> <option value="bed">using a list of intervals from a BED dataset</option> @@ -45,7 +42,7 @@ <option value="man">by chromosomes/contigs and coordinates</option> </param> <when value="bed"> - <param format="bed" label="BED file" name="input_interval" type="data" help="BED datasets can be obtained using "Get Data -> UCSC Main" datasource."/> + <param name="input_interval" type="data" format="bed" label="BED file" help="BED datasets can be obtained using "Get Data -> UCSC Main" datasource" /> </when> <when value="chr"> <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."> @@ -75,49 +72,43 @@ <param name="start" type="integer" min="1" value="0" label="Enter START coordinate (1-based)"/> <param name="end" type="integer" min="1" value="100" label="Enter END coordinate"/> </repeat> - - </when> </conditional> - </inputs> <outputs> - <data format="bam" name="output_bam" /> + <data name="output_bam" format="bam" /> </outputs> <tests> <test> - <param ftype="bam" name="input_bam" value="bam-slice-input.bam" /> + <param name="input_bam" ftype="bam" value="bam-slice-input.bam" /> <param name="slice_method_selector" value="bed"/> - <param ftype="bed" name="input_interval" value="bam-slice.bed" /> - <output file="bam-slice-test1.bam" ftype="bam" name="output_bam" /> + <param name="input_interval" ftype="bed" value="bam-slice.bed" /> + <output name="output_bam" file="bam-slice-test1.bam" ftype="bam" /> </test> <test> - <param ftype="bam" name="input_bam" value="bam-slice-input.bam" /> + <param name="input_bam" ftype="bam" value="bam-slice-input.bam" /> <param name="slice_method_selector" value="chr"/> <param name="refs" value="chrM" /> - <output file="bam-slice-test2.bam" ftype="bam" name="output_bam" /> + <output name="output_bam" file="bam-slice-test2.bam" ftype="bam" /> </test> <test> - <param ftype="bam" name="input_bam" value="bam-slice-input.bam" /> + <param name="input_bam" ftype="bam" value="bam-slice-input.bam" /> <param name="slice_method_selector" value="man"/> <param name="chrom" value="chrM" /> <param name="start" value="1" /> <param name="end" value="1000" /> - <output file="bam-slice-test3.bam" ftype="bam" name="output_bam" /> + <output name="output_bam" file="bam-slice-test3.bam" ftype="bam" /> </test> </tests> - <help> -<![CDATA[ - + <help><![CDATA[ **What it does** -Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates. BED datasets can be obtained from **Get Data -> UCSC Main**. +Allows to restrict (slice) input BAM dataset to a list of intervals defined in a BED file, individual chromosomes, or manually set list of coordinates. +BED datasets can be obtained from **Get Data -> UCSC Main**. This tool is based on ``samtools view`` command. @no-chrom-options@ - -]]> - </help> - <expand macro="citations"></expand> + ]]></help> + <expand macro="citations"/> </tool>
--- a/tool_dependencies.xml Tue Apr 21 17:37:49 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>