Mercurial > repos > artbio > lumpy_sv
diff lumpy.xml @ 6:48e97429a749 draft default tip
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_sv commit 37c0f0938a5cad74c954a89827a6a08bbbb81cb0
| author | artbio |
|---|---|
| date | Mon, 08 Jul 2024 22:23:10 +0000 |
| parents | 6ae3a402b9af |
| children |
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--- a/lumpy.xml Sun May 24 18:48:46 2020 -0400 +++ b/lumpy.xml Mon Jul 08 22:23:10 2024 +0000 @@ -1,9 +1,9 @@ -<tool id="lumpy" name="lumpy-sv" version="1.2.2"> +<tool id="lumpy" name="lumpy-sv" version="1.3"> <description>find structural variants</description> <requirements> - <requirement type="package" version="0.2.13">lumpy-sv</requirement> - <requirement type="package" version="1.3.1">samtools</requirement> - <requirement type="package" version="1.11.2=py27_0">numpy</requirement> + <requirement type="package" version="0.3.1">lumpy-sv</requirement> + <requirement type="package" version="1.18">samtools</requirement> + <requirement type="package" version="1.16.5">numpy</requirement> </requirements> <stdio> <exit_code range="1:" level="fatal" description="Tool exception" /> @@ -33,7 +33,7 @@ |python $__tool_directory__/pairend_distro.py -r $analysis_type.readLength -X 4 -N $seq_method.additional_params.samplingValue -o input.lib.histo > meandev.txt && mean=\$(cat meandev.txt | sed s/mean:// | sed -r s/stdev:.+//) && stdev=\$(cat meandev.txt | sed -r s/mean:.+stdev://) && - lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt + lumpy $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt #if $output_format == "BEDPE": -b #end if @@ -41,7 +41,7 @@ -sr id:'$one_sample_bam',bam_file:input.splitters.bam,back_distance:$seq_method.additional_params.back_distance,weight:$seq_method.additional_params.weight,min_mapping_threshold:$seq_method.additional_params.min_mapping_threshold > '$vcf_call' #elif $seq_method.seq_method_list == "single-read": samtools view -@ \${GALAXY_SLOTS:-4} -h '$one_sample_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam && - lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt + lumpy $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt #if $output_format == "BEDPE": -b #end if @@ -61,7 +61,7 @@ meanB=\$(cat meandevB.txt | sed s/mean:// | sed -r s/stdev:.+//) && stdevA=\$(cat meandevA.txt | sed -r s/mean:.+stdev://) && stdevB=\$(cat meandevB.txt | sed -r s/mean:.+stdev://) && - lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt + lumpy $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt #if $output_format == "BEDPE": -b #end if @@ -72,7 +72,7 @@ #elif $seq_method.seq_method_list == "single-read": samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_a_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.splitters.bam && samtools view -@ \${GALAXY_SLOTS:-4} -h '$sample_b_bam' | python $__tool_directory__/extractSplitReads_BwaMem.py -i stdin | samtools sort -@ \${GALAXY_SLOTS:-4} -O bam -o input.B.splitters.bam && - lumpy $seq_method.additional_params.evidence $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt + lumpy $seq_method.additional_params.probability_curve -mw $seq_method.additional_params.mw -tt $seq_method.additional_params.tt #if $output_format == "BEDPE": -b #end if @@ -116,7 +116,6 @@ <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> <param name="probability_curve" argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="true" label="output probability curve for each variant"/> - <param name="evidence" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="true" label="show evidence for each call"/> </section> </when> <when value="single-read"> @@ -127,7 +126,6 @@ <param name="weight" value="1" type="integer" label="weight" help="e.g. 1" /> <param name="min_mapping_threshold" value="20" type="integer" label="min_mapping_threshold" help="e.g. 20" /> <param name="probability_curve" argument="-P" type="boolean" truevalue="-P" falsevalue="" checked="false" label="output probability curve for each variant"/> - <param name="evidence" argument="-e" type="boolean" truevalue="-e" falsevalue="" checked="false" label="show evidence for each call"/> </section> </when> @@ -139,21 +137,21 @@ </inputs> <outputs> - <data format="tabular" name="histogram" label="Lumpy on ${on_string}: Fragment size distribution" from_work_dir="input.lib.histo"> + <data format="tabular" name="histogram" label="Lumpy-sv: Fragment size distribution" from_work_dir="input.lib.histo"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> - <data format="tabular" name="histogramB" label="Lumpy on ${on_string}: Fragment size distribution" from_work_dir="input.B.lib.histo"> + <data format="tabular" name="histogramB" label="Lumpy-sv: FragmentB size distribution" from_work_dir="input.B.lib.histo"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> <data format="bam" name="splits" label="Lumpy on ${on_string}: Split Reads (Bam format)" from_work_dir="input.splitters.bam"/> - <data format="bam" name="splitsB" label="Lumpy on ${on_string}: Split Reads (Bam format)" from_work_dir="input.B.splitters.bam"> + <data format="bam" name="splitsB" label="Lumpy on ${on_string}: SplitB Reads (Bam format)" from_work_dir="input.B.splitters.bam"> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> <data format="bam" name="discordants" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.discordants.bam"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> </data> - <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: Discordant Pairs (Bam format)" from_work_dir="input.B.discordants.bam"> + <data format="bam" name="discordantsB" label="Lumpy on ${on_string}: DiscordantB Pairs (Bam format)" from_work_dir="input.B.discordants.bam"> <filter>seq_method['seq_method_list'] == "paired-end"</filter> <filter>analysis_type['analysis_type_list'] == "two_sample"</filter> </data> @@ -165,7 +163,7 @@ </outputs> <tests> - <test> + <test expect_num_outputs="7"> <param name="analysis_type_list" value="two_sample" /> <param name="input_file" value="sample_Del.bam" ftype="bam"/> <param name="input_fileB" value="sample_cle.bam" ftype="bam"/> @@ -177,7 +175,7 @@ <param name="min_mapping_threshold" value="20" /> <output name="vcf_call" file="output_two.paired_end.vcf" ftype="vcf"/> </test> - <test> + <test expect_num_outputs="2"> <param name="analysis_type_list" value="one_sample" /> <param name="input_file" value="sr.input.bam" ftype="bam"/> <param name="seq_method_list" value="single-read" /> @@ -188,7 +186,7 @@ <param name="min_mapping_threshold" value="20" /> <output name="vcf_call" file="output.vcf" ftype="vcf"/> </test> - <test> + <test expect_num_outputs="2"> <param name="analysis_type_list" value="one_sample" /> <param name="input_file" value="sr.input.bam" ftype="bam"/> <param name="seq_method_list" value="single-read" /> @@ -197,11 +195,10 @@ <param name="back_distance" value="10"/> <param name="weight" value="1" /> <param name="min_mapping_threshold" value="20" /> - <param name="evidence" value="true" /> <param name="probability_curve" value="true" /> <output name="vcf_call" file="output_extended.vcf" ftype="vcf" compare="sim_size"/> </test> - <test> + <test expect_num_outputs="3"> <param name="analysis_type_list" value="two_sample" /> <param name="input_file" value="sr.input.bam" ftype="bam"/> <param name="input_fileB" value="sr.input.bam" ftype="bam"/>