# HG changeset patch # User iuc # Date 1619556531 0 # Node ID 17b378303f2de3d4f7ed5548d32725c1d7ec8421 # Parent 29151e779524e717b997a405d7d1022227dee473 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 3199d3f9c401663ffe45a679c3918489d4f6d149" diff -r 29151e779524 -r 17b378303f2d purge_dups.xml --- a/purge_dups.xml Tue Mar 09 18:25:07 2021 +0000 +++ b/purge_dups.xml Tue Apr 27 20:48:51 2021 +0000 @@ -2,16 +2,20 @@ and haplotigs in an assembly based on read depth (purge_dups) 1.2.5 - 1 + 2 purge_dups ./input.paf.gz && - #end if + #for $i, $file in enumerate($function_select.input): + #if $file.is_of_type("paf"): + gzip -c '${file}' > '${i}.gz' && + #else + ln -s '${file}' '${i}.gz' && + #end if + #end for purge_dups #if $function_select.coverage: -c '$function_select.coverage' @@ -46,11 +50,10 @@ #if $function_select.max_extend: -E $function_select.max_extend #end if - #if $function_select.input.is_of_type("paf"): - 'input.paf.gz' > dups.bed 2> purge_dups.log - #else: - '${function_select.input}' > dups.bed 2> purge_dups.log - #end if + #for $i, $file in enumerate($function_select.input): + '${i}.gz' + #end for + > dups.bed 2> purge_dups.log #else if $function_select.functions == "split_fa": split_fa #if $function_select.split: @@ -58,9 +61,13 @@ #end if '$function_select.input' > split.fasta #else if $function_select.functions == "pbcstat": - #if $function_select.input.is_of_type("paf"): - gzip -c '$function_select.input' > ./input.paf.gz && - #end if + #for $i, $file in enumerate($function_select.input): + #if $file.is_of_type("paf"): + gzip -c '${file}' > '${i}.gz' && + #else + ln -s '${file}' '${i}.gz' && + #end if + #end for pbcstat #if $function_select.max_cov: -M $function_select.max_cov @@ -75,11 +82,9 @@ -l $function_select.flank #end if $function_select.primary_alignments - #if $function_select.input.is_of_type("paf"): - 'input.paf.gz' - #else: - '${function_select.input}' - #end if + #for $i, $file in enumerate($function_select.input): + '${i}.gz' + #end for #else if $function_select.functions == "ngscstat": ngscstat #if $function_select.min_align_qual: @@ -137,7 +142,7 @@ - + @@ -163,7 +168,7 @@ - + @@ -288,6 +293,14 @@ + + + + + + + + @@ -325,6 +338,15 @@ + + + + + + + + + diff -r 29151e779524 -r 17b378303f2d test-data/out2.cov --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out2.cov Tue Apr 27 20:48:51 2021 +0000 @@ -0,0 +1,13 @@ +>gi|528476637:29857558-29915771 58214 +1 29092 0 +29093 29357 2 +29358 33375 0 +33376 41952 1 +41953 58214 0 +>gi|157734152:29655295-29712160 56866 +1 29213 0 +29214 29478 1 +29479 33497 0 +33498 42074 1 +42075 48470 0 +48471 56866 1 diff -r 29151e779524 -r 17b378303f2d test-data/out2.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out2.wig Tue Apr 27 20:48:51 2021 +0000 @@ -0,0 +1,116 @@ +track type="wiggle_0" name="PB" +fixedStep chrom=gi|528476637:29857558-29915771 start=1 step=1024 span=1024 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +1 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +variableStep chrom=gi|528476637:29857558-29915771 span=1894 +56321 0 +fixedStep chrom=gi|157734152:29655295-29712160 start=1 step=1024 span=1024 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +1 +1 +0 +0 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +variableStep chrom=gi|157734152:29655295-29712160 span=1570 +55297 1 diff -r 29151e779524 -r 17b378303f2d test-data/purge_dups_out_2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/purge_dups_out_2.bed Tue Apr 27 20:48:51 2021 +0000 @@ -0,0 +1,1 @@ +gi|157734152 29655294 29712160 HAPLOTIG gi|528476637 diff -r 29151e779524 -r 17b378303f2d test-data/test2.paf.gz Binary file test-data/test2.paf.gz has changed