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Valid choices are: pynast, infernal, clustalw, muscle, infernal, mafft [default: pynast]\" name=\"alignment_method\" optional=\"True\" type=\"select\">\n+\t\t\t<option selected=\"True\" value=\"None\">Selection is Optional</option>\n+\t\t\t<option value=\"pynast\">pynast</option>\n+\t\t\t<option value=\"infernal\">infernal</option>\n+\t\t\t<option value=\"clustalw\">clustalw</option>\n+\t\t\t<option value=\"muscle\">muscle</option>\n+\t\t\t<option value=\"infernal\">infernal</option>\n+\t\t\t<option value=\"mafft\">mafft</option>\n+\t\t</param>\n+\t\t<param label=\"-a/--pairwise_alignment_method: method for performing pairwise alignment in PyNAST. Valid choices are muscle, pair_hmm, clustal, blast, uclust, mafft [default: uclust]\" name=\"pairwise_alignment_method\" optional=\"True\" type=\"select\">\n+\t\t\t<option selected=\"True\" value=\"None\">Selection is Optional</option>\n+\t\t\t<option value=\"muscle\">muscle</option>\n+\t\t\t<option value=\"pair_hmm\">pair_hmm</option>\n+\t\t\t<option value=\"clustal\">clustal</option>\n+\t\t\t<option value=\"blast\">blast</option>\n+\t\t\t<option value=\"uclust\">uclust</option>\n+\t\t\t<option value=\"mafft\">mafft</option>\n+\t\t</param>\n+\t\t<param default=\"/home12/caparmor/bioinfo/softs/sources/Qiime/data/core_set_aligned.fasta.imputed\" label=\"-t/--template_fp: Filepath for template alignment [default: /home12/caparmor/bioinfo/softs/sources/Qiime/data/core_set_aligned.fasta.imputed]\" name=\"template_fp\" optional=\"True\" 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qiime workflow xml wrappers .\r\nI deleted the tgz in/output option and choose which options can be specified on the xml wrappers.\r\n\r\nFor the pick_otus.py wrapper, I modified how the clustering options are displayed (eg. swarm options are displayed if swarm is selected for the clustering, uclust options displayed if uclust is selected etc...)\r\nI selected 6 of the 12 clustering methods (those are the most interesting for our team) : uclust, uclust_ref, swarm, usearch, usearch_ref and 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