# HG changeset patch # User bgruening # Date 1482414017 18000 # Node ID a81b012ef352e65352fe551814a55cc3b0fc0a47 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/graphclust commit 11e50007837b1efa01a3039c92df0ebf63f0f7e9 diff -r 000000000000 -r a81b012ef352 dir2html.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dir2html.py Thu Dec 22 08:40:17 2016 -0500 @@ -0,0 +1,37 @@ +#!/usr/bin/env python +import os +import sys +from xml.sax.saxutils import escape + +def make_table( directory ): + ret = ['\n'] + for root, dirs, files in os.walk( directory ): + root = root.rstrip('/') + ret.append(' \n' % escape( os.path.split(root)[-1] )) + for file in files: + ret.append(' \n' % ( os.path.join( os.path.split(root)[-1], file), escape(file) )) + ret.append('
%s
%s
') + return ''.join(ret) + +def make_html( directory ): + return '\n'.join(['' + '', + ' Search results', + ' ', + '', + '', + '

Search Results

', + make_table( directory ), + '', + '']) + +if __name__ == '__main__': + if len(sys.argv) == 2: + directory_path = sys.argv[1] + else: top = '.' + print make_html( directory_path ) + diff -r 000000000000 -r a81b012ef352 graphclust.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/graphclust.xml Thu Dec 22 08:40:17 2016 -0500 @@ -0,0 +1,244 @@ + + alignment-free structural clustering of local RNA secondary structures + + GraphClust + locarna + RNAShapes + cmfinder + infernal + rnaz + vienna_rna + + + $output +]]> + + + + GLOBAL_group_size $GLOBAL_group_size + GLOBAL_hit_blacklist_overlap $GLOBAL_hit_blacklist_overlap + GLOBAL_iterations $GLOBAL_iterations + GLOBAL_num_clusters $GLOBAL_num_clusters + GLOBAL_plfold_minlen $GLOBAL_plfold_minlen + + OPTS_RNAfold --noLP + OPTS_RNAplfold --noLP -c $RNAplfold_c -L $RNAplfold_L -W $RNAplfold_W + OPTS_fasta2shrep_gspan -t "3=0,5=80" -M 5 -c 20 -win 40,150 -shift 30 --cue -u --stack --seq-graph-t --seq-graph-alph + OPTS_locarna_maligs -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --alifold-consensus-dp + OPTS_locarna_model -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --alifold-consensus-dp + OPTS_locarna_p_model -p $locarna_p --max-diff-am $locarna_max_diff_am --tau 100 --max-diff $locarna_max_diff --struct-weight $locarna_struct_weight --plfold-span 150 --plfold-winsize 200 --temperature $locarna_temperature --mea-beta 400 --consistency-transformation + OPTS_locarna_paligs -p $locarna_p --max-diff-am $locarna_max_diff_am --tau $locarna_tau --max-diff $locarna_max_diff --indel-open $locarna_indel_open --indel $locarna_indel --struct-weight $locarna_struct_weight + OPTS_nspdk -R $nspdk_R -D $nspdk_R -gt $nspdk_gt + OPTS_nspdk_centers -ensf 5 -oc -usn + + center_model_type 5 + center_subtree_max 7 + center_subtree_min 3 + center_tree_aligs 2 + center_tree_type 3 + cm_bitscore_sig 1 + cm_calibrate 0 + cm_max_eval 0.001 + cm_min_bitscore 15 + cm_top_only 0 + evaluate 0 + evaluate_class0_as_fp 0 + evaluate_min_overlap 0.51 + input_add_revcompl 0 + input_blastclust 1 + input_blastclust_id 90 + input_blastclust_len 0.90 + input_seq_min_length $other_input_seq_min_length + input_win_shift $other_input_win_shift + input_win_size 0 + nspdk_fcs 1 + nspdk_greylist_num 0 + nspdk_knn_center 10 + nspdk_nhf 500 + nspdk_nhf_max 1000 + nspdk_nhf_step 50 + results_merge_cluster_ol 0.66 + results_merge_overlap 0.51 + results_min_cluster_size $other_results_min_cluster_size + results_partition_type soft + results_top_num 10 + + + + + + + + + + + + + + +## OPTS_RNAfold --noLP + + + + + +##OPTS_RNAplfold --noLP + +##OPTS_fasta2shrep_gspan -t "3=0,5=80" -M 5 -c 20 -win 40,150 -shift 30 --cue -u --stack --seq-graph-t --seq-graph-alph + + + + + + + + + + + +##OPTS_locarna_maligs -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --alifold-consensus-dp +##OPTS_locarna_model -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --alifold-consensus-dp +##OPTS_locarna_p_model -p 0.001 --max-diff-am 50 --tau 100 --max-diff 100 --struct-weight 180 --plfold-span 150 --plfold-winsize 200 --temperature 180 --mea-beta 400 --consistency-transformation +##OPTS_locarna_paligs -p 0.001 --max-diff-am 50 --tau 50 --max-diff 100 --indel-open -400 --indel -200 --struct-weight 180 + + + + + + + + + + + + + + +#OPTS_nspdk -R 3 -D 3 -gt DIRECTED +#OPTS_nspdk_centers -ensf 5 -oc -usn + + + + + + +##center_model_type 5 +##center_subtree_max 7 +##center_subtree_min 3 +##center_tree_aligs 2 +##center_tree_type 3 +##cm_bitscore_sig 1 +##cm_calibrate 0 +##cm_max_eval 0.001 +##cm_min_bitscore 15 +##cm_top_only 0 +##evaluate 0 +##evaluate_class0_as_fp 0 +##evaluate_min_overlap 0.51 +##input_add_revcompl 0 +##input_blastclust 1 +##input_blastclust_id 90 +##input_blastclust_len 0.90 +##input_seq_min_length 50 +##input_win_shift 33 +##input_win_size 0 +##nspdk_fcs 1 +##nspdk_greylist_num 0 +##nspdk_knn_center 10 +##nspdk_nhf 500 +##nspdk_nhf_max 1000 +##nspdk_nhf_step 50 +##results_merge_cluster_ol 0.66 +##results_merge_overlap 0.51 +##results_min_cluster_size 5 +##results_partition_type soft +##results_top_num 10 + + + + + + + + + + 10.1093/bioinformatics/bts224 + +