Mercurial > repos > devteam > samtools_phase
annotate samtools_phase.xml @ 1:2523cb0fb84c draft
Uploaded tool version 1.0.1, updated for samtools 1.0.
| author | devteam |
|---|---|
| date | Wed, 24 Sep 2014 12:49:59 -0400 |
| parents | a0af255e28c1 |
| children | 2656247b5253 |
| rev | line source |
|---|---|
|
1
2523cb0fb84c
Uploaded tool version 1.0.1, updated for samtools 1.0.
devteam
parents:
0
diff
changeset
|
1 <tool id="samtools_phase" name="Call and phase" version="1.0.1"> |
| 0 | 2 <description>heterozygous SNPs</description> |
| 3 <requirements> | |
|
1
2523cb0fb84c
Uploaded tool version 1.0.1, updated for samtools 1.0.
devteam
parents:
0
diff
changeset
|
4 <requirement type="package" version="1.0">samtools</requirement> |
| 0 | 5 </requirements> |
| 6 <command>samtools phase -b "phase_wrapper" | |
| 7 #if str($option_set.option_sets) == 'advanced': | |
| 8 ${option_set.ignore_chimeras} | |
| 9 -k $option_set.block_length | |
| 10 -q $option_set.min_het | |
| 11 -Q $option_set.min_bq | |
| 12 -D $option_set.read_depth | |
| 13 ${option_set.drop_ambiguous} | |
| 14 #else | |
| 15 -k 13 -q 37 -Q 13 -D 256 | |
| 16 #end if | |
| 17 "$input_bam" > "$phase_sets" | |
| 18 </command> | |
| 19 <stdio> | |
| 20 <exit_code range="1:" level="fatal" description="Error" /> | |
| 21 </stdio> | |
| 22 <inputs> | |
| 23 <param format="bam" name="input_bam" type="data" label="Select dataset to phase"/> | |
| 24 <conditional name="option_set"> | |
| 25 <param name="option_sets" type="select" label="Phase parameters"> | |
| 26 <option value="default">Use defaults</option> | |
| 27 <option value="advanced">Advanced options</option> | |
| 28 </param> | |
| 29 <when value="default" /> | |
| 30 <when value="advanced"> | |
| 31 <param name="block_length" type="integer" value="13" label="Maximum length for local phasing" /> | |
| 32 <param name="min_het" type="integer" value="37" label="Minimum Phred-scaled level of detail to call a heterozygote" /> | |
| 33 <param name="min_bq" type="integer" value="13" label="Minimum base quality to be used in het calling" /> | |
| 34 <param name="read_depth" type="integer" value="256" label="Read depth" /> | |
| 35 <param name="ignore_chimeras" type="boolean" truevalue="-F" falsevalue="" checked="False" label="Do not attempt to fix chimeric reads" /> | |
| 36 <param name="drop_ambiguous" type="boolean" truevalue="-A 1" falsevalue="" checked="False" label="Drop reads with ambiguous phase" /> | |
| 37 </when> | |
| 38 </conditional> | |
| 39 </inputs> | |
| 40 <outputs> | |
| 41 <data format="txt" name="phase_sets" /> | |
| 42 <data format="bam" from_work_dir="phase_wrapper.0.bam" name="phase0" label="${tool.name} on ${on_string}: Phase-0 reads" /> | |
| 43 <data format="bam" from_work_dir="phase_wrapper.1.bam" name="phase1" label="${tool.name} on ${on_string}: Phase-1 reads" /> | |
| 44 <data format="bam" from_work_dir="phase_wrapper.chimeras.bam" name="chimera" label="${tool.name} on ${on_string}: Chimeric reads" /> | |
| 45 </outputs> | |
| 46 <tests> | |
| 47 <test> | |
| 48 <param name="option_sets" value="default" /> | |
| 49 <param name="input_bam" value="samtools_phase_in_1.bam" /> | |
| 50 <output name="phase_sets" file="samtools_phase_out_1_log.txt" ftype="txt" /> | |
| 51 <output name="phase0" file="samtools_phase_out_1_phase0.bam" ftype="bam" /> | |
| 52 <output name="phase1" file="samtools_phase_out_1_phase1.bam" ftype="bam" /> | |
| 53 <output name="chimera" file="empty_file.bam" compare="contains" /> | |
| 54 </test> | |
| 55 <test> | |
| 56 <param name="input_bam" value="samtools_phase_in_2.bam" /> | |
| 57 <param name="option_sets" value="advanced" /> | |
| 58 <param name="option_set|block_length" value="13" /> | |
| 59 <param name="option_set|min_het" value="37" /> | |
| 60 <param name="option_set|min_bq" value="13" /> | |
| 61 <param name="option_set|read_depth" value="256" /> | |
| 62 <param name="option_set|ignore_chimeras" value="false" /> | |
| 63 <param name="option_set|drop_ambiguous" value="true" /> | |
| 64 <output name="phase_sets" file="samtools_phase_out_2_log.txt" ftype="txt" /> | |
| 65 <output name="phase0" file="samtools_phase_out_2_phase0.bam" ftype="bam" /> | |
| 66 <output name="phase1" file="samtools_phase_out_2_phase1.bam" ftype="bam" /> | |
| 67 <output name="chimera" file="empty_file.bam" compare="contains" /> | |
| 68 </test> | |
| 69 <test> | |
| 70 <param name="input_bam" value="samtools_phase_in_2.bam" /> | |
| 71 <param name="option_sets" value="advanced" /> | |
| 72 <param name="option_set|block_length" value="13" /> | |
| 73 <param name="option_set|min_het" value="37" /> | |
| 74 <param name="option_set|min_bq" value="13" /> | |
| 75 <param name="option_set|read_depth" value="256" /> | |
| 76 <param name="option_set|ignore_chimeras" value="true" /> | |
| 77 <param name="option_set|drop_ambiguous" value="false" /> | |
| 78 <output name="phase_sets" file="samtools_phase_out_3_log.txt" ftype="txt" /> | |
| 79 <output name="phase0" file="samtools_phase_out_3_phase0.bam" ftype="bam" /> | |
| 80 <output name="phase1" file="samtools_phase_out_3_phase1.bam" ftype="bam" /> | |
| 81 <output name="chimera" file="empty_file.bam" compare="contains" /> | |
| 82 </test> | |
| 83 </tests> | |
| 84 <help> | |
| 85 **What it does** | |
| 86 | |
| 87 Call and phase heterozygous SNPs | |
| 88 | |
| 89 ------ | |
| 90 | |
| 91 .. list-table:: **Options** | |
| 92 :widths: 5 5 40 10 | |
| 93 :header-rows: 1 | |
| 94 | |
| 95 * - Flag | |
| 96 - Type | |
| 97 - Description | |
| 98 - Default | |
| 99 * - -k | |
| 100 - INT | |
| 101 - Block length | |
| 102 - 13 | |
| 103 * - -b | |
| 104 - STR | |
| 105 - Prefix of BAM file output | |
| 106 - *null* | |
| 107 * - -q | |
| 108 - INT | |
| 109 - Minimum het phred-LOD | |
| 110 - 37 | |
| 111 * - -Q | |
| 112 - INT | |
| 113 - Min base quality in het calling | |
| 114 - 13 | |
| 115 * - -D | |
| 116 - INT | |
| 117 - Max read depth | |
| 118 - 256 | |
| 119 * - -D | |
| 120 - BOOLEAN | |
| 121 - Do not attempt to fix chimeras | |
| 122 - *off* | |
| 123 * - -A | |
| 124 - BOOLEAN | |
| 125 - Drop reads with ambiguous phase | |
| 126 - *off* | |
| 127 | |
| 128 ------ | |
| 129 | |
| 130 **Citation** | |
| 131 | |
| 132 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>`_ | |
| 133 | |
| 134 | |
| 135 If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* | |
| 136 | |
| 137 </help> | |
| 138 </tool> |