# 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
+ ]]>
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+ ]]>
@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