# HG changeset patch # User iuc # Date 1611325923 0 # Node ID 6184cfc70e28aa71cf7816f9f6b5bf8d472297f0 # Parent 9919057a466c1d2408f163ffcde903e7fc8fec3d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit d18d984264f54b45e94d97b5b97ed499a32a334a" diff -r 9919057a466c -r 6184cfc70e28 filter.xml --- a/filter.xml Thu Oct 29 20:50:57 2020 +0000 +++ b/filter.xml Fri Jan 22 14:32:03 2021 +0000 @@ -8,12 +8,12 @@ 'sample.bcf.gz' && - bcftools index 'sample.bcf.gz' && +#if $input.is_of_type('vcf') + bcftools view -Ob '$input' > 'input.bcf.gz' && + bcftools index 'input.bcf.gz' && #else - ln -s '${samples}' 'sample.bcf.gz' && - ln -s '${samples.metadata.bcf_index}' 'sample.bcf.gz.csi' && + ln -s '${input}' 'input.bcf.gz' && + ln -s '${input.metadata.bcf_index}' 'input.bcf.gz.csi' && #end if ## run @@ -31,38 +31,37 @@ --samples '$sv.mode_cond.samples' --coverage $sv.mode_cond.coverage --controlcontamination $sv.mode_cond.controlcontamination -#end if ## germline options -#if $sv.mode_cond.mode_sel == 'germline' +#else if $sv.mode_cond.mode_sel == 'germline' --gq $sv.mode_cond.gq --rddel $sv.mode_cond.rddel --rddup $sv.mode_cond.rddup #end if -## samples -'sample.bcf.gz' ## input +## input +'input.bcf.gz' ## postprocessing @LOG@ @VCF@ ]]> - +
- - + +
- + - - + + @@ -72,23 +71,23 @@
-
+
+ -
- + - +
@@ -113,7 +112,7 @@ - +
@@ -137,6 +136,11 @@ + + + + + @@ -144,15 +148,10 @@ - - - - - - +
@@ -176,7 +175,7 @@ - +
@@ -200,6 +199,11 @@ + + + + + @@ -207,15 +211,10 @@ - - - - - - +
@@ -227,7 +226,7 @@
- + @@ -246,8 +245,6 @@ @WID@ -Delly *filter* contains workflows for germline and somatic SV calling. - **Input** *Somatic* filtering requires a called SV input with at least one tumor sample and a matched control sample. In addition, a tab-delimited sample description needs to be provided, in which the first column holds the sample ids (as found in the VCF/BCF input) and the second column specifies either tumor or control. @@ -256,7 +253,7 @@ **Output** -The output is available in BCF and VCF format. +The output is available in BCF and VCF format. Additionally a log file is provided. .. class:: infomark diff -r 9919057a466c -r 6184cfc70e28 macros.xml --- a/macros.xml Thu Oct 29 20:50:57 2020 +0000 +++ b/macros.xml Fri Jan 22 14:32:03 2021 +0000 @@ -1,6 +1,6 @@ - 0.8.5 + 0.8.7 0 @@ -17,14 +17,12 @@ - + - + + + + + + + - + + + + + + + + + + - - + + - - - - - - - + - - + + + + + - - + + + + + + - - + - + + + + 'bcf' in oo['out'] + + 'vcf' in oo['out'] - - - 'bcf' in oo['out'] - - 'dump' in oo['out'] @@ -116,12 +125,25 @@ - + `_.