# HG changeset patch
# User sanbi-uwc
# Date 1549979813 18000
# Node ID 9963e812cd1da0f2cb099206657343d04dcae105

planemo upload for repository https://github.com/COMBAT-TB/confil commit a15dc3aa51957af76127510e78cb47871bd7666f

diff -r 000000000000 -r 9963e812cd1d confil.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/confil.xml	Tue Feb 12 08:56:53 2019 -0500
@@ -0,0 +1,49 @@
+<tool id="confil" name="Contamination Filter (confil)" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="7.0">click</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        confil --threads $threads --paired --cutoff $cutoff "$input1" "$input2"
+    ]]></command>
+    <inputs>
+        <param type="data" name="input1" format="fastq" />
+        <param type="data" name="input2" format="fastq" />
+        <param name="cutoff" type="integer" label="Cutoff percentage" 
+               value="50" min="50" max="99" />
+        <param name="threads" type="integer" label="Number of threads" 
+               value="1" min="1" max="4" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular" from_work_dir="seq.report" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="seq_1.fastq"/>
+            <param name="input2" value="seq_2.fastq"/>
+            <output name="output1" file="seq.report"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Usage: confil [OPTIONS] SEQFILES...
+
+Options:
+  --db PATH          Name for Kraken 2 DB  [default:
+                     /tools/databases/kraken2/04092018/standard/; required]
+  --threads INTEGER  Number of threads  [default: 1]
+  --cutoff INTEGER   Percentage of fragments covered  [default: 90]
+  --paired           The filenames provided have paired-end reads
+  --help             Show this message and exit.
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubconfil,
+  author = {SANBI-SA},
+  year = {2019},
+  title = {confil},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/COMBAT-TB/confil},
+}</citation>
+    </citations>
+</tool>
diff -r 000000000000 -r 9963e812cd1d test-data/seq.report
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seq.report	Tue Feb 12 08:56:53 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
diff -r 000000000000 -r 9963e812cd1d test-data/seq_1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seq_1.fastq	Tue Feb 12 08:56:53 2019 -0500
@@ -0,0 +1,16 @@
+@seq1
+AGTCGTGGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_?abcdefghijklmno
+@seq2
+AGTCGTTGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+;>@BCElcH@KLMNOPQ>STZVWbYu[\]^_?a=;d?fghijklmno
+@seq3
+AGTCGTCGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+7>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_?abcdefghijklmno
+@seq4
+AGTCGTAGTCATCGTGACTAGTCGATCTAGCTAGCTCTCTAGAGTGT
++
+;>@BCEFGHJKLMNOPQRSTUVWXYZ[\]^_?abcdefghijklmno
diff -r 000000000000 -r 9963e812cd1d test-data/seq_2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/seq_2.fastq	Tue Feb 12 08:56:53 2019 -0500
@@ -0,0 +1,24 @@
+@seq1
+AAAGGTTTCTCTTTTGGAAATATCTAAATCCC
++
+!"#$%&\'()*+,-./0123456789:;<=>.
+@seq2
+GGGTCTCCCAGAATGATTAGAGCCGTATAGGA
++
+?@ABCDEFGHIJK MNOPQRSTUVWXYZ[\\]
+@seq3
+GCGGTTCAATACGATTACCACCATGATAAATA
++
+?Aa.1ghB2K!#lk(02GY[[II])Kwl+,5M
+@seq4
+AGTCTTTTCCTCTAAAATAACATAGGATACTA
++
+ghY)N375Nh.,Ol>==/<:2#i&d%#KdNII
+@seq5
+GAGGACTCATGGTAGGTATTTTACATGACATT
++
+IIgy%hf6#394bd&hNMWL$OPB63II*,+-
+@seq6
+GGCCTACATTCATTTACGAGACTAATTAGGGA
++
+IIIIIgd6#5%jKO&.,D+s3aW=cdGB#a1$
\ No newline at end of file