| Previous changeset 1:03627f24605f (2020-01-31) Next changeset 3:3b4b2121842f (2020-03-21) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lofreq commit 3d0fa6bbfa1ee35ab1de444703741cc90f95c729" |
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modified:
lofreq_call.xml |
| b |
| diff -r 03627f24605f -r dfadc322b065 lofreq_call.xml --- a/lofreq_call.xml Fri Jan 31 06:18:45 2020 -0500 +++ b/lofreq_call.xml Wed Feb 12 18:45:42 2020 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="lofreq_call" name="Call variants" version="@WRAPPER_VERSION@0">\n+<tool id="lofreq_call" name="Call variants" version="@TOOL_VERSION@+galaxy1">\n <description>with LoFreq</description>\n <macros>\n <import>macros.xml</import>\n@@ -9,6 +9,28 @@\n @PREPARE_REF@\n ln -s \'$reads\' reads.bam &&\n ln -s -f \'${reads.metadata.bam_index}\' reads.bam.bai &&\n+ #if str($call_control.set_call_options) == \'yes\':\n+ #set $ign_vcfs = []\n+ #if str($call_control.source_qual.use_src_qual.src_qual):\n+ #for $n, $ign_vcf in enumerate($call_control.source_qual.use_src_qual.ign_vcf):\n+ ## lofreq recognizes compressed vcf input based on its .gz\n+ ## suffix => symlink all datasets with standard extensions.\n+ ## For bgzipped vcfs, also make the index files available.\n+ #if $ign_vcf:\n+ #if $ign_vcf.is_of_type(\'vcf_bgzip\'):\n+ #set $ign_src = \'ign%d.vcf.gz\' % $n\n+ ln -s \'$ign_vcf\' $ign_src &&\n+ ln -s \'$ign_vcf.metadata.tabix_index\' ${ign_src}.tbi &&\n+ #else:\n+ #set $ign_src = \'ign%d.vcf\' % $n\n+ ln -s \'$ign_vcf\' $ign_src &&\n+ #end if\n+ #silent $ign_vcfs.append($ign_src)\n+ #end if\n+ #end for\n+ #end if\n+ #set $ign_vcfs = \',\'.join($ign_vcfs)\n+ #end if\n \n ## call variants with lofreq\n \n@@ -30,21 +52,33 @@\n --max-depth $call_control.coverage.max_depth\n $call_control.pe.use_orphan\n --min-bq $call_control.bc_quals.min_bq\n- --min-alt-bq $call_control.bc_quals.min_alt_bq\n- --def-alt-bq $call_control.bc_quals.def_alt_bq\n+ #if $call_control.bc_quals.min_alt_bq > $call_control.bc_quals.min_bq:\n+ --min-alt-bq $call_control.bc_quals.min_alt_bq\n+ #else:\n+ --min-alt-bq $call_control.bc_quals.min_bq\n+ #end if\n+ #if str($call_control.bc_quals.alt_bq.modify):\n+ --def-alt-bq $call_control.bc_quals.alt_bq.def_alt_bq\n+ #end if\n ${call_control.align_quals.alnqual.use_alnqual}\n #if str($call_control.align_quals.alnqual.use_alnqual) != \'-A -B\':\n ${call_control.align_quals.alnqual.alnqual_choice.alnquals_to_use}\n ${call_control.align_quals.alnqual.alnqual_choice.extended_baq}\n #end if\n --min-mq $call_control.map_quals.min_mq\n- --max-mq $call_control.map_quals.use_mq.max_mq\n- $call_control.map_quals.use_mq.no_mq\n+ #if str($call_control.map_quals.use_mq.no_mq):\n+ $call_control.map_quals.use_mq.no_mq\n+ #else:\n+ #if $call_control.map_quals.use_mq.max_mq > $call_control.map_quals.min_mq:\n+ --max-mq $call_control.map_quals.use_mq.max_mq\n+ #else:\n+ --max-mq $call_control.map_quals.min_mq\n+ #end if\n+ #end if\n #if str($call_control.source_qual.use_src_qual.src_qual):\n $call_control.source_qual.use_src_qual.src_qual\n- #set $ign_vcfs = \',\'.join([str($ign_vcf) for $ign_vcf in $call_control.source_qual.use_src_qual.ign_vcf if $ign_vcf])\n #if $ign_vcfs:\n- --ign-vcf "$ign_vcfs"\n+ --ign-vcf \'$ign_vcfs\'\n #end if\n --def-nm-q $call_control.source_qual.use_src_qual.def_nm_q\n #end if\n@@ -125,9 +159,23 @@\n <param name="min_alt_bq" argument="--min-alt-bq" type="integer" min="0" value="6"\n label="Minimum baseQ for alternate bases"\n help="For variant calling at'..b' Note: The special MAPQ value 255 is used by many tools to indicate undefined mapping quality, and lofreq call will ignore such reads during variant calling. Capping, however, will turn 255 into a regular MAPQ score. Thus, if you need to avoid using such reads, you should filter out MAPQ 255 reads from your input data with other tools before using lofreq call with MAPQ capping."/>\n+ help="For the joint quality model at any site, cap the mapping quality of reads at this value (default: 255 = do not cap mapping qualities). Notes: 1) You cannot cap mapping qualities at less than the minimum MAPQ defined above. If you try, MAPQs will be capped at that minimum quality instead. 2) The special MAPQ value 255 is used by many tools to indicate undefined mapping quality, and lofreq call will ignore such reads during variant calling. Capping, however, will turn 255 into a regular MAPQ score. Thus, if you need to avoid using such reads, you should filter out MAPQ 255 reads from your input data with other tools before using lofreq call with MAPQ capping."/>\n </when>\n <when value="--no-mq">\n <param name="max_mq" type="hidden" value="" />\n@@ -179,7 +227,7 @@\n <param name="def_nm_q" argument="--def-nm-q" type="integer" min="-1" value="-1"\n label="Replace non-match base qualities with this value"\n help="For the calculation of the source quality, replace all base qualities of non-match bases with this value (default: -1 = use original base qualities)." />\n- <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf" optional="true" multiple="true"\n+ <param name="ign_vcf" argument="--ign-vcf" type="data" format="vcf,vcf_bgzip" optional="true" multiple="true"\n label="VCF input(s) with variants to ignore for source quality computation"\n help="Mismatches caused by known true variants in your samples should not lower the source quality estimate. If any read in your input has a base that is non-reference, but supports one of the known variants in the specified VCF datasets, that base will not be treated as a mismatch." />\n </when>\n@@ -248,6 +296,31 @@\n <param name="reads" ftype="bam" value="lofreq-in1.bam" />\n <param name="ref_selector" value="history" />\n <param name="ref" ftype="fasta" value="pBR322.fa" />\n+ <conditional name="call_control">\n+ <param name="set_call_options" value="yes" />\n+ </conditional>\n+ <output name="variants" file="call-out1.vcf" lines_diff="4" />\n+ </test>\n+ <test>\n+ <param name="reads" ftype="bam" value="lofreq-in1.bam" />\n+ <param name="ref_selector" value="history" />\n+ <param name="ref" ftype="fasta" value="pBR322.fa" />\n+ <conditional name="call_control">\n+ <param name="set_call_options" value="yes" />\n+ <section name="source_qual">\n+ <conditional name="use_src_qual">\n+ <param name="src_qual" value="--src-qual" />\n+ <param name="def_nm_q" value="40" />\n+ <param name="ign_vcf" ftype="vcf" value="call-out1.vcf" />\n+ </conditional>\n+ </section>\n+ </conditional>\n+ <output name="variants" file="call-out1.vcf" lines_diff="4" />\n+ </test>\n+ <test>\n+ <param name="reads" ftype="bam" value="lofreq-in1.bam" />\n+ <param name="ref_selector" value="history" />\n+ <param name="ref" ftype="fasta" value="pBR322.fa" />\n <conditional name="filter_control">\n <param name="filter_type" value="set_all_off" />\n </conditional>\n' |