Mercurial > repos > sanbi-uwc > confil
changeset 0:9963e812cd1d draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit a15dc3aa51957af76127510e78cb47871bd7666f
author | sanbi-uwc |
---|---|
date | Tue, 12 Feb 2019 08:56:53 -0500 |
parents | |
children | d5b37a19547a |
files | confil.xml test-data/seq.report test-data/seq_1.fastq test-data/seq_2.fastq |
diffstat | 4 files changed, 105 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /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>
--- /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
--- /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
--- /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