# HG changeset patch # User sanbi-uwc # Date 1550066561 18000 # Node ID d5b37a19547a8aa693a49c1ff64955286aa71a9c # Parent 9963e812cd1da0f2cb099206657343d04dcae105 planemo upload for repository https://github.com/COMBAT-TB/confil commit 8239f5a11e0d9be3fb2b95e5c0241677da722bb9 diff -r 9963e812cd1d -r d5b37a19547a confil.xml --- a/confil.xml Tue Feb 12 08:56:53 2019 -0500 +++ b/confil.xml Wed Feb 13 09:02:41 2019 -0500 @@ -3,24 +3,53 @@ click + confil --threads $threads + #set $input_type = $input_type_conditional.input_type + #if $input_type == "paired_collection" + --paired + #end if + --cutoff $cutoff + #if $input_type == "single" + "${input_type_conditional.single_input}" + #elif $input_type == "paired_collection" + "${input_type_conditional.collection_input.forward}" "${input_type_conditional.collection_input.reverse}" + #end if + ]]> + - - - - + + + + + + + + + + + + + + - + - - - + + + + + + + + + + + + + + ]]> @misc{githubconfil, diff -r 9963e812cd1d -r d5b37a19547a test-data/seq.report --- a/test-data/seq.report Tue Feb 12 08:56:53 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,16 +0,0 @@ - 28.34 1198200 1198200 U 0 unclassified - 71.66 3030398 1705 R 1 root - 71.59 3027326 90 R1 131567 cellular organisms - 71.33 3016097 5832 D 2 Bacteria - 56.09 2371684 139 D1 1783272 Terrabacteria group - 55.96 2366280 32 P 201174 Actinobacteria - 55.96 2366229 970 C 1760 Actinobacteria - 55.90 2363912 491 O 85007 Corynebacteriales - 55.88 2363031 1244 F 1762 Mycobacteriaceae - 55.84 2361413 2074448 G 1763 Mycobacterium - 6.64 280596 161419 G1 77643 Mycobacterium tuberculosis complex - 2.50 105696 74351 S 1773 Mycobacterium tuberculosis - 0.16 6824 6824 S1 747369 Mycobacterium tuberculosis R1207 - 0.03 1383 827 S1 83332 Mycobacterium tuberculosis H37Rv - 0.01 266 266 S2 757419 Mycobacterium tuberculosis H37RvCO - \ No newline at end of file diff -r 9963e812cd1d -r d5b37a19547a test-data/seq.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/seq.tab Wed Feb 13 09:02:41 2019 -0500 @@ -0,0 +1,16 @@ + 28.34 1198200 1198200 U 0 unclassified + 71.66 3030398 1705 R 1 root + 71.59 3027326 90 R1 131567 cellular organisms + 71.33 3016097 5832 D 2 Bacteria + 56.09 2371684 139 D1 1783272 Terrabacteria group + 55.96 2366280 32 P 201174 Actinobacteria + 55.96 2366229 970 C 1760 Actinobacteria + 55.90 2363912 491 O 85007 Corynebacteriales + 55.88 2363031 1244 F 1762 Mycobacteriaceae + 55.84 2361413 2074448 G 1763 Mycobacterium + 6.64 280596 161419 G1 77643 Mycobacterium tuberculosis complex + 2.50 105696 74351 S 1773 Mycobacterium tuberculosis + 0.16 6824 6824 S1 747369 Mycobacterium tuberculosis R1207 + 0.03 1383 827 S1 83332 Mycobacterium tuberculosis H37Rv + 0.01 266 266 S2 757419 Mycobacterium tuberculosis H37RvCO + \ No newline at end of file