| Next changeset 1:8bfe0d1616d2 (2015-11-11) |
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Commit message:
Uploaded tool and dependency definition. |
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added:
samtools_phase.xml test-data/empty_file.bam test-data/samtools_phase_in_1.bam test-data/samtools_phase_in_2.bam test-data/samtools_phase_out_1_log.txt test-data/samtools_phase_out_1_phase0.bam test-data/samtools_phase_out_1_phase1.bam test-data/samtools_phase_out_2_log.txt test-data/samtools_phase_out_2_phase0.bam test-data/samtools_phase_out_2_phase1.bam test-data/samtools_phase_out_3_log.txt test-data/samtools_phase_out_3_phase0.bam test-data/samtools_phase_out_3_phase1.bam tool_dependencies.xml |
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| diff -r 000000000000 -r cba1944e3ed0 samtools_phase.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/samtools_phase.xml Thu Mar 27 15:26:17 2014 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r cba1944e3ed0 test-data/samtools_phase_in_2.bam |
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| Binary file test-data/samtools_phase_in_2.bam has changed |
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| diff -r 000000000000 -r cba1944e3ed0 test-data/samtools_phase_out_1_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_phase_out_1_log.txt Thu Mar 27 15:26:17 2014 -0400 |
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| @@ -0,0 +1,30 @@ +CC +CC Descriptions: +CC +CC CC comments +CC PS start of a phase set +CC FL filtered region +CC M[012] markers; 0 for singletons, 1 for phased and 2 for filtered +CC EV supporting reads; SAM format +CC // end of a phase set +CC +CC Formats of PS, FL and M[012] lines (1-based coordinates): +CC +CC PS chr phaseSetStart phaseSetEnd +CC FL chr filterStart filterEnd +CC M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1 +CC +CC +PS chrI 1187 1290 +M1 chrI 1187 1187 T A 1 2 0 4 0 +M1 chrI 1187 1216 T A 2 3 0 4 0 +M1 chrI 1187 1222 C A 3 3 0 3 1 +M1 chrI 1187 1290 A T 4 1 0 0 0 +EV 0 chrI 1 40 3M * 0 0 AAC * YP:i:1 YF:i:0 YI:i:2 YO:i:1 YS:i:1164 +EV 0 chrI 1 40 3M * 0 0 TTC * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1141 +EV 0 chrI 1 40 3M * 0 0 AAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1147 +EV 0 chrI 1 40 3M * 0 0 AAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1176 +EV 0 chrI 1 40 3M * 0 0 TTC * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1157 +EV 0 chrI 1 40 3M * 0 0 AAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1145 +EV 0 chrI 2 40 3M * 0 0 TCA * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1215 +// |
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| diff -r 000000000000 -r cba1944e3ed0 test-data/samtools_phase_out_1_phase0.bam |
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| diff -r 000000000000 -r cba1944e3ed0 test-data/samtools_phase_out_2_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_phase_out_2_log.txt Thu Mar 27 15:26:17 2014 -0400 |
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| @@ -0,0 +1,65 @@ +CC +CC Descriptions: +CC +CC CC comments +CC PS start of a phase set +CC FL filtered region +CC M[012] markers; 0 for singletons, 1 for phased and 2 for filtered +CC EV supporting reads; SAM format +CC // end of a phase set +CC +CC Formats of PS, FL and M[012] lines (1-based coordinates): +CC +CC PS chr phaseSetStart phaseSetEnd +CC FL chr filterStart filterEnd +CC M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1 +CC +CC +PS chrI 1412 1542 +M1 chrI 1412 1412 T C 1 7 0 9 0 +M1 chrI 1412 1414 G A 2 7 0 9 0 +M1 chrI 1412 1421 G A 3 7 0 9 0 +M1 chrI 1412 1471 T C 4 5 0 6 0 +M1 chrI 1412 1542 C T 5 3 0 2 0 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1340 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1374 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1346 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1366 +EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1409 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1359 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1353 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1343 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1379 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1350 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1389 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1348 +EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1407 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1358 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1341 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1392 +EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1462 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1468 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1444 +EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1457 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1461 +// +PS chrI 3611 3731 +M1 chrI 3611 3611 T A 6 5 0 4 0 +M1 chrI 3611 3659 C T 7 9 0 6 0 +M1 chrI 3611 3731 T A 8 4 0 1 1 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3578 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3590 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3571 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3576 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3559 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3568 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3609 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3651 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3647 +EV 0 chrI 7 40 2M * 0 0 TA * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3644 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3644 +EV 0 chrI 7 40 2M * 0 0 TT * YP:i:1 YF:i:0 YI:i:1 YO:i:1 YS:i:3657 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3637 +// |
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| diff -r 000000000000 -r cba1944e3ed0 test-data/samtools_phase_out_2_phase1.bam |
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| diff -r 000000000000 -r cba1944e3ed0 test-data/samtools_phase_out_3_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_phase_out_3_log.txt Thu Mar 27 15:26:17 2014 -0400 |
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| @@ -0,0 +1,65 @@ +CC +CC Descriptions: +CC +CC CC comments +CC PS start of a phase set +CC FL filtered region +CC M[012] markers; 0 for singletons, 1 for phased and 2 for filtered +CC EV supporting reads; SAM format +CC // end of a phase set +CC +CC Formats of PS, FL and M[012] lines (1-based coordinates): +CC +CC PS chr phaseSetStart phaseSetEnd +CC FL chr filterStart filterEnd +CC M? chr PS pos allele0 allele1 hetIndex #supports0 #errors0 #supp1 #err1 +CC +CC +PS chrI 1412 1542 +M1 chrI 1412 1412 T C 1 7 0 9 0 +M1 chrI 1412 1414 G A 2 7 0 9 0 +M1 chrI 1412 1421 G A 3 7 0 9 0 +M1 chrI 1412 1471 T C 4 5 0 6 0 +M1 chrI 1412 1542 C T 5 3 0 2 0 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1340 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1374 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1346 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1366 +EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1409 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1359 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1353 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1343 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1379 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1350 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1389 +EV 0 chrI 1 40 3M * 0 0 CAA * YP:i:1 YF:i:0 YI:i:3 YO:i:0 YS:i:1348 +EV 0 chrI 1 40 4M * 0 0 TGGT * YP:i:0 YF:i:0 YI:i:4 YO:i:0 YS:i:1407 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1358 +EV 0 chrI 1 40 3M * 0 0 TGG * YP:i:0 YF:i:0 YI:i:3 YO:i:0 YS:i:1341 +EV 0 chrI 1 40 4M * 0 0 CAAC * YP:i:1 YF:i:0 YI:i:4 YO:i:0 YS:i:1392 +EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1462 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1468 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1444 +EV 0 chrI 4 40 2M * 0 0 CT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:1457 +EV 0 chrI 4 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:1461 +// +PS chrI 3611 3731 +M1 chrI 3611 3611 T A 6 5 0 4 0 +M1 chrI 3611 3659 C T 7 9 0 6 0 +M1 chrI 3611 3731 T A 8 4 0 1 1 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3578 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3590 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3571 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3576 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3559 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3569 +EV 0 chrI 6 40 2M * 0 0 AT * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3568 +EV 0 chrI 6 40 2M * 0 0 TC * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3609 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3651 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3647 +EV 0 chrI 7 40 2M * 0 0 TA * YP:i:1 YF:i:0 YI:i:2 YO:i:0 YS:i:3644 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3644 +EV 0 chrI 7 40 2M * 0 0 TT * YP:i:1 YF:i:0 YI:i:1 YO:i:1 YS:i:3657 +EV 0 chrI 7 40 2M * 0 0 CT * YP:i:0 YF:i:0 YI:i:2 YO:i:0 YS:i:3637 +// |
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| diff -r 000000000000 -r cba1944e3ed0 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Mar 27 15:26:17 2014 -0400 |
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| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="samtools" version="0.1.19"> + <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |