Mercurial > repos > devteam > samtools_phase
changeset 5:2311187710fb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_phase commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
| author | iuc |
|---|---|
| date | Tue, 09 May 2017 11:16:22 -0400 |
| parents | ee06ec9cf0a6 |
| children | dd8305e4e58e |
| files | macros.xml samtools_phase.xml tool_dependencies.xml |
| diffstat | 3 files changed, 28 insertions(+), 71 deletions(-) [+] |
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--- a/macros.xml Fri Dec 18 19:45:25 2015 -0500 +++ b/macros.xml Tue May 09 11:16:22 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>echo $(samtools --version | head -n 1)", "$(samtools --version | grep -o -E "htslib.*?")</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_phase.xml Fri Dec 18 19:45:25 2015 -0500 +++ b/samtools_phase.xml Tue May 09 11:16:22 2017 -0400 @@ -1,12 +1,13 @@ -<tool id="samtools_phase" name="Call and phase" version="2.0"> +<tool id="samtools_phase" name="Call and phase" version="2.0.1"> <description>heterozygous SNPs</description> <macros> - <import>macros.xml</import> - </macros> - <expand macro="requirements"></expand> - <expand macro="stdio"></expand> - <expand macro="version_command"></expand> - <command>samtools phase -b "phase_wrapper" + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + samtools phase -b phase_wrapper #if str($option_set.option_sets) == 'advanced': ${option_set.ignore_chimeras} -k $option_set.block_length @@ -15,10 +16,13 @@ -D $option_set.read_depth ${option_set.drop_ambiguous} #else - -k 13 -q 37 -Q 13 -D 256 + -k 13 + -q 37 + -Q 13 + -D 256 #end if - "$input_bam" > "$phase_sets" - </command> + '$input_bam' > '$phase_sets' + ]]></command> <inputs> <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/> <conditional name="option_set"> @@ -28,12 +32,12 @@ </param> <when value="default" /> <when value="advanced"> - <param name="block_length" type="integer" value="13" label="Maximum length for local phasing" /> - <param name="min_het" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" /> - <param name="min_bq" type="integer" value="13" label="Minimum base quality to be used in het calling" /> - <param name="read_depth" type="integer" value="256" label="Read depth" /> - <param name="ignore_chimeras" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" /> - <param name="drop_ambiguous" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" /> + <param name="block_length" argument="-k" type="integer" value="13" label="Maximum length for local phasing" /> + <param name="min_het" argument="-q" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" /> + <param name="min_bq" argument="-Q" type="integer" value="13" label="Minimum base quality to be used in het calling" /> + <param name="read_depth" argument="-D" type="integer" value="256" label="Read depth" /> + <param name="ignore_chimeras" argument="-F" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" /> + <param name="drop_ambiguous" argument="-A" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" /> </when> </conditional> </inputs> @@ -81,50 +85,10 @@ <output name="chimera" file="empty_file.bam" compare="contains" /> </test> </tests> - <help> + <help><![CDATA[ **What it does** -Call and phase heterozygous SNPs - ------- - -.. list-table:: **Options** - :widths: 5 5 40 10 - :header-rows: 1 - - * - Flag - - Type - - Description - - Default - * - -k - - INT - - Block length - - 13 - * - -b - - STR - - Prefix of BAM file output - - *null* - * - -q - - INT - - Minimum het phred-LOD - - 37 - * - -Q - - INT - - Min base quality in het calling - - 13 - * - -D - - INT - - Max read depth - - 256 - * - -D - - BOOLEAN - - Do not attempt to fix chimeras - - *off* - * - -A - - BOOLEAN - - Drop reads with ambiguous phase - - *off* - - </help> - <expand macro="citations"></expand> +Call and phase heterozygous SNPs. + ]]></help> + <expand macro="citations"/> </tool>
--- a/tool_dependencies.xml Fri Dec 18 19:45:25 2015 -0500 +++ /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="a55970300738" name="package_samtools_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>