Mercurial > repos > devteam > samtools_phase
diff samtools_phase.xml @ 0:a0af255e28c1 draft
Imported from capsule None
author | devteam |
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date | Wed, 12 Mar 2014 12:45:41 -0400 |
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children | 2523cb0fb84c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_phase.xml Wed Mar 12 12:45:41 2014 -0400 @@ -0,0 +1,138 @@ +<tool id="samtools_phase" name="Call and phase" version="1.0.0"> + <description>heterozygous SNPs</description> + <requirements> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <command>samtools phase -b "phase_wrapper" + #if str($option_set.option_sets) == 'advanced': + ${option_set.ignore_chimeras} + -k $option_set.block_length + -q $option_set.min_het + -Q $option_set.min_bq + -D $option_set.read_depth + ${option_set.drop_ambiguous} + #else + -k 13 -q 37 -Q 13 -D 256 + #end if + "$input_bam" > "$phase_sets" + </command> + <stdio> + <exit_code range="1:" level="fatal" description="Error" /> + </stdio> + <inputs> + <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/> + <conditional name="option_set"> + <param name="option_sets" type="select" label="Phase parameters"> + <option value="default">Use defaults</option> + <option value="advanced">Advanced options</option> + </param> + <when value="default" /> + <when value="advanced"> + <param name="block_length" type="integer" value="13" label="Maximum length for local phasing" /> + <param name="min_het" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" /> + <param name="min_bq" type="integer" value="13" label="Minimum base quality to be used in het calling" /> + <param name="read_depth" type="integer" value="256" label="Read depth" /> + <param name="ignore_chimeras" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" /> + <param name="drop_ambiguous" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="phase_sets" /> + <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" /> + <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" /> + <data format="bam" from_work_dir="phase_wrapper.chimeras.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" /> + </outputs> + <tests> + <test> + <param name="option_sets" value="default" /> + <param name="input_bam" value="samtools_phase_in_1.bam" /> + <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" /> + <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" /> + <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" /> + <output name="chimera" file="empty_file.bam" compare="contains" /> + </test> + <test> + <param name="input_bam" value="samtools_phase_in_2.bam" /> + <param name="option_sets" value="advanced" /> + <param name="option_set|block_length" value="13" /> + <param name="option_set|min_het" value="37" /> + <param name="option_set|min_bq" value="13" /> + <param name="option_set|read_depth" value="256" /> + <param name="option_set|ignore_chimeras" value="false" /> + <param name="option_set|drop_ambiguous" value="true" /> + <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" /> + <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" /> + <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" /> + <output name="chimera" file="empty_file.bam" compare="contains" /> + </test> + <test> + <param name="input_bam" value="samtools_phase_in_2.bam" /> + <param name="option_sets" value="advanced" /> + <param name="option_set|block_length" value="13" /> + <param name="option_set|min_het" value="37" /> + <param name="option_set|min_bq" value="13" /> + <param name="option_set|read_depth" value="256" /> + <param name="option_set|ignore_chimeras" value="true" /> + <param name="option_set|drop_ambiguous" value="false" /> + <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" /> + <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" /> + <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" /> + <output name="chimera" file="empty_file.bam" compare="contains" /> + </test> + </tests> + <help> +**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* + +------ + +**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> +</tool>