I'm looking at a run of PHAC's SRST2 wrapper:
/srv/galaxy/var/shed_tools/toolshed.g2.bx.psu.edu/repos/nml/srst2/e59fdf6145db/srst2/srst2.pl /data/galaxy/jobs/020/20188/outputs/dataset_cef3ef2e-e010-4768-b36b-1de43d89b28f.dat /data/galaxy/jobs/020/20188/outputs/dataset_582ba0b2-a2eb-4918-a8b2-9f300b6f212a.dat /data/galaxy/jobs/020/20188/outputs/dataset_d6eec7c7-a2c9-4bcd-a919-63b192c9935e.dat g /data/galaxy/jobs/020/20188/outputs/dataset_14d30ba8-5d8d-4237-a672-243227aac1d7.dat /data/galaxy/jobs/020/20188/outputs/dataset_473b25c9-757c-4a56-8170-df8add14378b.dat \
"ResFinder.fasta,ARGannot_r2.fasta" \
"SRX6855211_SRR10127028_1.fastq uncompressed" \
--input_pe "/data/galaxy/f/e/1/dataset_fe1245a6-287d-4732-af60-37021f7eaab1.dat" \
"/data/galaxy/5/6/e/dataset_56eedb18-918a-4c26-a5db-f3504dd763c2.dat" \
--gene_db /data/galaxy/1/6/2/dataset_162c6169-c72f-4f07-a99d-dfd15075ab8e.dat /data/galaxy/5/6/d/dataset_56da7859-6beb-47cd-b701-3b9bcae0e427.dat \
--gene_max_mismatch 250 --read_type q --save_scores --other "'-p ${GALAXY_SLOTS:-1}'" --output ${PWD}/out
(line breaks manually inserted for clarity)
However the output sample table has only part of the sample identifier:
Column 1 Column 2 Column 3 Column 4 Column 5 Column 6 Column 7 Column 8 Column 9 Column 10 Column 11 Column 12 Column 13 Column 14
Sample DB gene allele coverage depth diffs uncertainty divergence length maxMAF clusterid seqid annotation
SRX6855211 ARGannot_r2 AmpC2_Ecoli_Bla AmpC2_346 99.735 86.838 22snp3indel 1.94 1134 0.091 99 346 no;no;AmpC2;Bla;CP002970;332756-333889;1134
SRX6855211 ARGannot_r2 MrdA_Bla MrdA_836 100.0 66.382 25snp 1.314 1902 0.143 16 836 no;no;MrdA;Bla;CP002291;666340-664439;1902
SRX6855211 ARGannot_r2 MphA_MLS MphA_1663 100.0 69.11 0.0 906 0.096 158 1663 no;no;MphA;MLS;KR091911;890-1795;906
SRX6855211 ARGannot_r2 CTX-M-9_Bla CTX-M-27_109 100.0 60.304 0.0 876 0.078 190 109 no;no;CTX-M-27;Bla;AY156923;1-876;876
which means I can't match them back up with their input sample once they've gone through hamronize (which I really love.)
I'm looking at a run of PHAC's SRST2 wrapper:
(line breaks manually inserted for clarity)
However the output sample table has only part of the sample identifier:
which means I can't match them back up with their input sample once they've gone through hamronize (which I really love.)